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AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: In this software paper, Page et al develop ‘AlbaTraDIS’; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes.

Assessing the impact of introductory programming workshops on the computational reproducibility of biomedical workflows

Publishing date: 2020-08-18 Published on: PLOS ONE summary: This mixed methods study consisted of in-depth interviews with 14 biomedical researchers before and after participation in an introductory programming workshop. During the interviews, participants described their research workflows and responded to a quantitative checklist measuring reproducible behaviors.

bigPint: A Bioconductor visualization package that makes big data pint-sized

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: bigPint is a software package for interactive and static data visualisation in R. It scales comfortably to large datasets, sporting graphs that include scatterplots, violin plots, and litre plots.

GitHub Sealed Away Its Open Source Code In an Arctic Fault

Publishing date: 2020-08-18 Published on: Futurism summary: Earlier this month, the code management platform GitHub sealed away its archive of open source software in an Arctic vault so deep that they say it could survive a nuclear blast.

New Open-Source Software Looks To Kickstart The Autonomous Revolution

Publishing date: 2020-08-18 Published on: Forbes summary: This article reports on “https://www.project-aslan.org/">Project ASLAN<, a collaborative alternative to the tech race at the forefront of the move towards fully-autonomous vehicles. ASLAN is a supergroup of tech companies, research groups and universities, focused on bringing a fiscally practical, fully-autonomous vehicle solution to public roads.

OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: In this study, Butenko et al propose a new open-source simulation platform that comprises computer-aided design and computer-aided engineering tools for highly automated evaluation of electric field distribution and neural activation during Deep Brain Stimulation (DBS).

RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition

Publishing date: 2020-08-18 Published on: PLOS ONE summary: High throughput RNA-Seq has become a staple in modern molecular biology, with applications not only in quantifying gene expression but also in isoform-level analysis of the RNA transcripts.

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: In this report, Zimin and Salzberg present the assembly polishing tool POLCA (POLishing by Calling Alternatives) and compare its performance with two other popular polishing programs, Pilon and Racon.

This new open source project could be key to securing database applications

Publishing date: 2020-08-18 Published on: TechRepublic summary: Moving database applications to the cloud has been a boon for development teams anxious to move faster. It has also, however, exposed security flaws inherent in traditional security solutions, something data layer security startup Cyral has been tackling.

Open Hardware Makers

Publishing date: 2020-07-06 Published on: Open Hardware Makers summary: This program to teach and share open source hardware practices has just finished its pilot and is now seeking community feedback on it’s curriculum.

Development of a low-cost, user-customizable, high-speed camera

Publishing date: 2020-06-15 Published on: PLOS ONE summary: Channel Editor Summary: The paper describes a high speed camera system, capable of reaching frame rates of ~2300 frames per second in its max speed setting.

African scientists leverage open hardware

Publishing date: 2020-06-15 Published on: Nature summary: This article looks at how a growing emphasis on do-it-yourself science is helping researchers to equip labs in resource-limited areas. For example, “https://doi.org/10.1016/j.ohx.2018.e00047">Actifield< n automated open source actimeter for rodents developed by Victor Kumbol at the Kwame Nkrumah University of Science and Technology in Kumasi, Ghana.

Bottom-Illuminated Orbital Shaker for Microalgae Cultivation

Publishing date: 2020-06-15 Published on: bioRxiv summary: None authors: Jakub Nedbal, Lu Gao, Klaus Suhling link to paper: https://doi.org/10.1101/2020.05.01.071878 Icons made by catkuro from www.flaticon.com

DIY hybrid SSVEP-P300 LED stimuli for BCI platform using EMOTIV EEG headset

Publishing date: 2020-06-15 Published on: HardwareX summary: None authors: Sure jMouli, Ramaswamy Palaniappan link to paper: https://doi.org/10.1016/j.ohx.2020.e00113 Icons made by catkuro from www.flaticon.com

FishCam: A low-cost open source autonomous camera for aquatic research

Publishing date: 2020-06-15 Published on: HardwareX summary: In this work, Mouy et al describe the “FishCam”, a low-cost (500 USD) autonomous camera package to record videos and images underwater. The system is composed of easily accessible components and can be programmed to turn ON and OFF on customizable schedules.

Is open sourcing the next frontier in space exploration?

Publishing date: 2020-06-15 Published on: The Space Review summary: Innovations in scientific research and data analysis can propel us forward in the field of space exploration. This article explores how Open Source practices can be used to boost the rate of innovation in the software and hardware involved in space exploration.

Low-cost and precise inline pressure sensor housing and DAQ for use in laboratory experiments

Publishing date: 2020-06-15 Published on: Hardware X summary: None authors: Luke Goertzen, Nicole Mehr, Manuel Lopez, Chet Udell, John S.Selker link to paper: https://doi.org/10.1016/j.ohx.2020.e00112 Icons made by catkuro from www.flaticon.com

PlanktonScope: Affordable modular imaging platform for citizen oceanography

Publishing date: 2020-06-15 Published on: bioRxiv summary: None authors: Thibaut Pollina, Adam G. Larson, Fabien Lombard, Hongquan Li, Sebastien Colin, Colomban de Vargas, Manu Prakash link to paper: https://doi.org/10.1101/2020.04.23.056978 Icons made by catkuro from www.

SiCTeC: an inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging

Publishing date: 2020-06-15 Published on: bioRxiv summary: None authors: Benjamin D. Knapp, Lillian Zhu, Kerwyn Casey Huang link to paper: https://doi.org/10.1101/2020.05.29.123166 Icons made by catkuro from www.flaticon.com

The Incubot: A 3D Printer-Based Microscope for Long-Term Live Cell Imaging within a Tissue Culture Incubator

Publishing date: 2020-06-15 Published on: bioRxiv summary: Commercial live cell imaging systems represent a large financial burden to research groups, while current open source incubator microscopy systems lack adaptability and are sometimes inadequate for complex imaging experimentation.

The Science Cheep – #1

Publishing date: 2020-06-15 Published on: Lab On The Cheap summary: The Science Cheep, written for Lab On The Cheap, provides you with updates in the DIY open-source world of science from the past week.

TinyML is giving hardware new life

Publishing date: 2020-06-15 Published on: TechCrunch summary: None authors: Adam Benzion link to paper: https://techcrunch.com/2020/05/29/tinyml-is-giving-hardware-new-life/ Icons made by catkuro from www.flaticon.com

A practical 3D-printed soft robotic prosthetic hand with multi-articulating capabilities

Publishing date: 2020-05-14 Published on: PLOS ONE summary: None authors: Alireza Mohammadi, Jim Lavranos, Hao Zhou, Rahim Mutlu, Gursel Alici, Ying Tan, Peter Choong, Denny Oetomo link to paper: 10.1371/journal.pone.0232766

Open source meeting tools: 3 things to know

Publishing date: 2020-05-12 Published on: The Enterprisers Project summary: Are you considering an open source alternative to standard videoconferencing software? Here, the author reviews some of the options such as Jitsi, Jami, and Signal.

ProteinVR: Web-based molecular visualization in virtual reality

Publishing date: 2020-05-12 Published on: PLOS Computational Biology summary: Channel Editor Summary: Have you ever wondered what proteins look like? In fact, accurately conceptualizing 3D protein structures is vital to both scientific research and education.

Synchronized editing: the future of collaborative writing

Publishing date: 2020-05-12 Published on: Nature summary: Draft scientific manuscripts tend to be confidential, however this article presents the approach of Olga Botvinnik who managed her paper like a piece of open-source software.

Tech and Covid-19: open source needed for contact tracing apps

Publishing date: 2020-05-12 Published on: Information Age summary: The inevitable and necessary responses to COVID-19 from the lockdown itself, to the use of contact tracing apps raise concerns about our civil liberties that in a different time would all have been hotly debated over a considerable time period.

Leveraging open hardware to alleviate the burden of COVID-19 on global health systems

Publishing date: 2020-05-06 Published on: PLOS Biology summary: With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment.

Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis

Publishing date: 2020-04-27 Published on: PLOS Computational Biology summary: None authors: Yuanchao Zhang, Man S. Kim, Erin R. Reichenberger, Ben Stear, Deanne M. Taylor link to paper: 10.1371/journal.pcbi.1007794 Icons made by catkuro from www.

Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application

Publishing date: 2020-04-21 Published on: PLOS ONE summary: None authors: Kai Pua, Daisuke Yuhara, Sho Ayuba, Kenji Yasuoka link to paper: 10.1371/journal.pone.0231714 Icons made by catkuro from www.flaticon.com

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Publishing date: 2020-04-06 Published on: PLOS Computational Biology summary: None authors: Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, J. Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani

Leveraging open hardware to alleviate the burden of COVID-19 on global health systems

Publishing date: 2020-04-06 Published on: Preprints.org summary: In the global response to COVID-19 there is a shortfall of staffing, facilities, and equipment facing up to high demand for diagnosis, isolation, and treatment.

Open Source Hardware: The Rise of RISC-V

Publishing date: 2020-04-06 Published on: The New Stack summary: This article looks at “https://riscv.org”>RISC-V<. The RISC-V foundation provides a free and open source instruction set architecture for chips based on the long-established paradigms for reduced instruction set computing.

Open-Source Neuroscience Hardware Hack Chat

Publishing date: 2020-04-06 Published on: Hackaday summary: This article was written to promote the OPEN-SOURCE NEUROSCIENCE HARDWARE HACK CHAT that took place in February 2020, a transcript of which is available https://hackaday.

Open-source, 3D-printed Peristaltic Pumps for Small Volume Point-of-Care Liquid Handling

Publishing date: 2020-04-06 Published on: Scientific Reports summary: Microfluidic technologies are frequently employed as point-of-care diagnostic tools for improving time-to-diagnosis and improving patient outcomes in clinical settings. These microfluidic devices often are designed to operate with peripheral equipment for liquid handling that increases the cost and complexity of these systems and reduces their potential for widespread adoption in low resource healthcare applications.

Super‐beacons: Open‐source probes with spontaneous tuneable blinking compatible with live‐cell super‐resolution microscopy

Publishing date: 2020-04-06 Published on: Traffic summary: In this work Pereira et al present a new class of DNA‐based self‐quenching open‐source super‐resolution probes that they developed, named super beacons. These probes have photoswitching kinetics that can be tuned structurally, thermally and chemically.

Towards national policy for open source hardware research: The case of Finland

Publishing date: 2020-04-06 Published on: Technological Forecasting and Social Change summary: Free and open-source hardware (FOSH) is rapidly gaining momentum because it provides customized research hardware with over 90% savings compared to the costs of proprietary tools.

UC2 – A Versatile and Customizable low-cost 3D-printed Optical Open-Standard for microscopic imaging

Publishing date: 2020-04-06 Published on: bioRxiv summary: Channel Editor Summary: UC2 is an inexpensive 3D-printed microscopy toolbox that takes modular development seriously, they are a great example of a project that has thought through assembly standards, extensibility and operability from the start of their project and have some impressive assemblies capable of hologrpahic, confocal and light sheet microscopy.

BiteOscope: an open platform to study mosquito blood-feeding behavior

Publishing date: 2020-04-03 Published on: bioRxiv summary: None authors: Felix JH Hol, Louis Lambrechts, Manu Prakash link to paper: https://doi.org/10.1101/2020.02.19.955641 Icons made by catkuro from www.flaticon.com

LED Zappelin’: An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging | bioRxiv

Publishing date: 2020-04-03 Published on: bioRxiv summary: None authors: M.J.Y. Zimmermann, A.M. Chagas, P. Bartel, S. Pop, L.L. Prieto Godino, T. Baden link to paper: https://doi.org/10.1101/2020.03.10.986000 Icons made by catkuro from www.

microUSV: A low-cost platform for indoor marine swarm robotics research

Publishing date: 2020-04-03 Published on: Hardware X summary: None authors: Calvin Gregory, Andrew Vardy link to paper: https://doi.org/10.1016/j.ohx.2020.e00105 Icons made by catkuro from www.flaticon.com

Open-source five degree of freedom motion platform for investigating fish-robot interaction

Publishing date: 2020-04-03 Published on: Hardware X summary: None authors: Brent Utter, Alexander Brown link to paper: https://doi.org/10.1016/j.ohx.2020.e00107 Icons made by catkuro from www.flaticon.com

PlasPI marine cameras: Open-source, affordable camera systems for time series marine studies

Publishing date: 2020-04-03 Published on: Hardware X summary: None authors: Autun Purser, Ulrich Hoge, Johannes Lemburg, Yasemin Bodur, Elena Schiller, Janine Ludszuweit, Jens Greinert, Frank Wenzhöfer link to paper: https://doi.org/10.1016/j.ohx.2020.e00102

RPG: A low-cost, open-source, high-performance solution for displaying visual stimuli

Publishing date: 2020-04-03 Published on: bioRxiv summary: None authors: Vivian Imbriotis, Adam Ranson, William M Connelly link to paper: https://doi.org/10.1101/2020.03.05.979724 Icons made by catkuro from www.flaticon.com

SAFE Acoustics: an open-source, real-time eco-acoustic monitoring network in the tropical rainforests of Borneo

Publishing date: 2020-04-03 Published on: bioRxiv summary: None authors: Sarab S. Sethi, Robert M. Ewers, Nick S. Jones, Aaron Signorelli, Lorenzo Picinali, C. David L. Orme link to paper: https://doi.org/10.1101/2020.02.27.968867

Ten simple rules for providing effective bioinformatics research support

Publishing date: 2020-03-26 Published on: PLOS Computational Biology summary: None authors: Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi, Lyndon Zass

Multiple social platforms reveal actionable signals for software vulnerability awareness: A study of GitHub, Twitter and Reddit

Publishing date: 2020-03-24 Published on: PLOS ONE summary: None authors: Prasha Shrestha, Arun Sathanur, Suraj Maharjan, Emily Saldanha, Dustin Arendt, Svitlana Volkova link to paper: 10.1371/journal.pone.0230250 Icons made by catkuro from www.

A portable, low-cost device for precise control of specimen temperature under stereomicroscopes

Publishing date: 2020-03-11 Published on: PLOS ONE summary: None authors: Nicholas D. Testa, Samiksha Kaul, Kim N. Le, Mei Zhan, Hang Lu, Annalise B. Paaby link to paper: 10.1371/journal.pone.0230241 Icons made by catkuro from www.

BornAgain: software for simulating and fitting grazing-incidence small-angle scattering

Publishing date: 2020-03-03 Published on: Journal of Applied Crystallography summary: BornAgain is a free and open-source multi-platform software framework for simulating and fitting X-ray and neutron reflectometry, off-specular scattering, and grazing-incidence small-angle scattering (GISAS).

Compressive Big Data Analytics: An Ensemble Meta-Algorithm for High-dimensional Multisource Datasets

Publishing date: 2020-03-03 Published on: bioRxiv summary: None authors: Simeone Marino, Yi Zhao, Nina Zhou, Yiwang Zhou, Arthur Toga, Lu Zhao, Yingsi Jian, Yichen Yang, Yehu Chen, Qiucheng Wu, Jessica Wild, Brandon Cummings, Ivo D.

HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes

Publishing date: 2020-03-03 Published on: GigaScience summary: Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality.

Metrics for graph comparison: A practitioner’s guide

Publishing date: 2020-03-03 Published on: PLOS ONE summary: Comparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience, cyber security, social network analysis, and bioinformatics.

Multi-template matching: a versatile tool for object-localization in microscopy images

Publishing date: 2020-03-03 Published on: BMC Bioinformatics summary: The localization of objects of interest is a key initial step in most image analysis workflows. For biomedical image data, classical image-segmentation methods like thresholding or edge detection are typically used.

PANEV: an R package for a pathway-based network visualization

Publishing date: 2020-03-03 Published on: BMC Bioinformatics summary: None authors: Valentino Palombo, Marco Milanesi, Gabriella Sferra, Stefano Capomaccio, Sandy Sgorlon & Mariasilvia D’Andrea link to paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7 Icons made by catkuro from www.

pyKNEEr: An image analysis workflow for open and reproducible research on femoral knee cartilage

Publishing date: 2020-03-03 Published on: PLOS ONE summary: Channel Editor Summary: Sometimes, all the available algorithms to perform a scientific task are either closed source, or just too complex to easily be re-used by others.

Repository-based plasmid design

Publishing date: 2020-03-03 Published on: PLOS ONE summary: There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU.

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data

Publishing date: 2020-03-03 Published on: PLOS Computational Biology summary: Ribosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics. This technique has been available for a decade, yet the current state and standardization of publicly available computational tools for these data is bleak.

RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method

Publishing date: 2020-02-14 Published on: PLOS Computational Biology summary: None authors: Kosuke Hamazaki, Hiroyoshi Iwata link to paper: 10.1371/journal.pcbi.1007663 Icons made by catkuro from www.flaticon.com

A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a

Publishing date: 2020-02-07 Published on: PLOS ONE summary: None authors: Florian Katzmeier, Lukas Aufinger, Aurore Dupin, Jorge Quintero, Matthias Lenz, Ludwig Bauer, Sven Klumpe, Dawafuti Sherpa, Benedikt Dürr, Maximilian Honemann, Igor Styazhkin, Friedrich C.

A plug-and-play Hyperspectral Imaging Sensor using low-cost equipment

Publishing date: 2020-02-07 Published on: Hardware X summary: Hyperspectral Imaging Sensors (HSI) obtain spectral information from an object, and they are used to solve problems in Remote Sensing, Food Analysis, Precision Agriculture, and others.

An arbitrary-spectrum spatial visual stimulator for vision research

Publishing date: 2020-02-07 Published on: eLife summary: Visual neuroscientists require accurate control of visual stimulation. However, few stimulator solutions offer high spatio-temporal resolution and free control over the spectra of the light sources, because they rely on off-the-shelf technology developed for human trichromatic vision.

An Open-Source, Automated Home-Cage Sipper Device for Monitoring Liquid Ingestive Behavior in Rodents

Publishing date: 2020-02-07 Published on: eNeuro summary: None authors: Elizabeth Godynyuk, Maya N. Bluitt, Jessica R. Tooley, Alexxai V. Kravitz and Meaghan C. Creed link to paper: https://www.eneuro.org/content/6/5/ENEURO.0292-19.2019 Icons made by catkuro from www.

CoralCam: A flexible, low-cost ecological monitoring platform

Publishing date: 2020-02-07 Published on: Hardware X summary: None authors: Austin Greene, Zac Forsman, Robert J. Toonen, Megan J. Donahue link to paper: https://doi.org/10.1016/j.ohx.2019.e00089 Icons made by catkuro from www.flaticon.com

Designing Tools for Civilization: The Future of Open Source Hardware

Publishing date: 2020-02-07 Published on: The Startup summary: This article presents the 2011 TED Talk of Marcin Jakubowski, the founder of “https://www.opensourceecology.org/">Open Source Ecology<, an open collaborative of engineers, producers, and builders.

ElectroPen: An ultra-low–cost, electricity-free, portable electroporator

Publishing date: 2020-02-07 Published on: PLOS Biology summary: None authors: Gaurav Byagathvalli, Soham Sinha, Yan Zhang, Mark P. Styczynski, Janet Standeven, M. Saad Bhamla link to paper: 10.1371/journal.pbio.3000589 Icons made by catkuro from www.

Exploiting open source 3D printer architecture for laboratory robotics to automate high-throughput time-lapse imaging for analytical microbiology

Publishing date: 2020-02-07 Published on: PLOS ONE summary: None authors: Sarah H. Needs, Tai The Diep, Stephanie P. Bull, Anton Lindley-Decaire, Partha Ray, Alexander D. Edwards link to paper: 10.1371/journal.pone.0224878

Fieldwork-based determination of design priorities for point-of-use drinking water quality sensors for use in resource-limited environments

Publishing date: 2020-02-07 Published on: PLOS ONE summary: None authors: Michael S. Bono Jr., Sydney Beasley, Emily Hanhauser, A. John Hart, Rohit Karnik, Chintan Vaishnav link to paper: 10.1371/journal.pone.0228140 Icons made by catkuro from www.

Manufacturers demand open 3D printing ecosystem, study shows

Publishing date: 2020-02-07 Published on: Product Engineering Solutions summary: This article reports on the findings of an independent global investigation of the current and future use of 3D printing. The study revealed that 995 of the manufacturing executives surveyed believe that an open ecosystem is important to advance 3D printing at scale.

One-shot phase-recovery using a cellphone RGB camera on a Jamin-Lebedeff microscope

Publishing date: 2020-02-07 Published on: PLOS ONE summary: None authors: Benedict Diederich, Barbora Marsikova, Brad Amos, Rainer Heintzmann link to paper: 10.1371/journal.pone.0227096 Icons made by catkuro from www.flaticon.com

Open Source Hardware Risks

Publishing date: 2020-02-07 Published on: Semiconductor Engineering summary: Open-source hardware is gaining attention on a variety of fronts, from chiplets and the underlying infrastructure to the ecosystems required to support open-source and hybrid open-source and proprietary designs.

Open-source 3D printed air-jet for generating monodispersed alginate microhydrogels

Publishing date: 2020-02-07 Published on: bioRxiv summary: None authors: Dustin J. Hadley, Kevin T. Campbell, Marina H. Gabriel, Eduardo A. Silva link to paper: https://www.biorxiv.org/content/10.1101/804849v2 Icons made by catkuro from www.

OptiJ: Open-source optical projection tomography of large organ samples

Publishing date: 2020-02-07 Published on: Scientific Reports summary: Channel Editor Summary: The second paper in this pairing, describes an optical projection tomography (OPT) system for large transparent organ samples. Capable of imaging high volumes (up to 13mm tall X8mm deep) at near-cellular resolution (50µm), they go beyond current low cost OPT by providing more than one solution to sample alignment issues present in these tyoes of systems.

Robotic microscopy for everyone: the OpenFlexure Microscope

Publishing date: 2020-02-07 Published on: bioRxiv summary: Channel Editor Summary: For this update the “editor’s pick” highlights two papers describing two different tools that leverage previous open designs, showing in practice the benefits of using open source hardware for scientific tool development.

SweepStat: A Build-It-Yourself, Two-Electrode Potentiostat for Macroelectrode and Ultramicroelectrode Studies

Publishing date: 2020-02-07 Published on: J. Chem. Educ summary: None authors: Matthew W. Glasscott, Matthew D. Verber, Jackson R. Hall, Andrew D. Pendergast, Collin J. McKinney, Jeffrey E. Dick link to paper: https://pubs.

The hottest thing in robotics is an open source project you’ve never heard of

Publishing date: 2020-02-07 Published on: TechRepublic summary: This article provides a summary of the history and future directions of “https://www.ros.org/">ROS<, the Robot Operating System. This project might not be well known, but it’s increasingly important for driving the robots used for industrial automation.

The smfBox: an open-source platform for single-molecule FRET

Publishing date: 2020-02-07 Published on: bioRxiv summary: Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules.

Want To Build An Open Source Hardware And Software Robot?

Publishing date: 2020-02-07 Published on: Design News summary: The 2020 Consumer Electronics Show “https://www.ces.tech/">CES< saw many engineering marvels revealed for the first time. At the conference “https://www.pollen-robotics.com/">Pollen Robotics< displayed their “Reachy” robot.

µPump: An open-source pressure pump for precision fluid handling in microfluidics

Publishing date: 2020-02-07 Published on: HardwareX summary: None authors: Run Ze Gao, Marie Hébert, Jan Huissoon, Carolyn L.Ren link to paper: https://www.sciencedirect.com/science/article/pii/S2468067220300043 Icons made by catkuro from www.flaticon.com

‘We need a people’s cryo-EM.’ Scientists hope to bring revolutionary microscope to the masses

Publishing date: 2020-02-07 Published on: Science summary: In 1962 LMB researchers won a Nobel Prize for using x-ray crystallography to decipher the first atomic structures for proteins. One of LMB’s most recent Nobel laureates, Richard Henderson, helped to develop cryo-EM a technique that bypasses the difficult process of forming crystals from proteins.

Orbit Image Analysis: An open-source whole slide image analysis tool

Publishing date: 2020-02-05 Published on: PLOS Computational Biology summary: None authors: Manuel Stritt, Anna K. Stalder, Enrico Vezzali link to paper: 10.1371/journal.pcbi.1007313 Icons made by catkuro from www.flaticon.com

LeMaRns: A Length-based Multi-species analysis by numerical simulation in R

Publishing date: 2020-02-03 Published on: PLOS ONE summary: None authors: Michael A. Spence, Hayley J. Bannister, Johnathan E. Ball, Paul J. Dolder, Christopher A. Griffiths, Robert B. Thorpe link to paper: 10.

An accurate, precise, and affordable light emitting diode spectrophotometer for drinking water and other testing with limited resources

Publishing date: 2020-01-29 Published on: PLOS ONE summary: None authors: Michael W. Prairie, Seth H. Frisbie, K. Kesava Rao, Anyamanee H. Saksri, Shreyas Parbat, Erika J. Mitchell link to paper: 10.

FlexGraph: Flexible partitioning and storage for scalable graph mining

Publishing date: 2020-01-24 Published on: PLOS ONE summary: None authors: Chiwan Park, Ha-Myung Park, U. Kang link to paper: 10.1371/journal.pone.0227032 Icons made by catkuro from www.flaticon.com

Knowledge-guided analysis of omics data using the KnowEnG cloud platform

Publishing date: 2020-01-23 Published on: PLOS Biology summary: None authors: Charles Blatti III, Amin Emad, Matthew J. Berry, Lisa Gatzke, Milt Epstein, Daniel Lanier, Pramod Rizal, Jing Ge, Xiaoxia Liao, Omar Sobh, Mike Lambert, Corey S.

A network-centric approach for estimating trust between open source software developers

Publishing date: 2020-01-15 Published on: PLOS ONE summary: None authors: Hitesh Sapkota, Pradeep K. Murukannaiah, Yi Wang link to paper: 10.1371/journal.pone.0226281 Icons made by catkuro from www.flaticon.com

Assemblage of Focal Species Recognizers—AFSR: A technique for decreasing false indications of presence from acoustic automatic identification in a multiple species context

Publishing date: 2020-01-15 Published on: PLOS ONE summary: None authors: Ivan Braga Campos, Todd J. Landers, Kate D. Lee, William George Lee, Megan R. Friesen, Anne C. Gaskett, Louis Ranjard

Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives

Publishing date: 2020-01-15 Published on: PLOS Genetics summary: None authors: Madison Caballero, Daniel N. Seidman, Ying Qiao, Jens Sannerud, Thomas D. Dyer, Donna M. Lehman, Joanne E. Curran, Ravindranath Duggirala, John Blangero, Shai Carmi, Amy L.

Diversity: Why open source needs to work on it in 2020 - TechRepublic

Publishing date: 2020-01-15 Published on: TechRepublic summary: This article discusses the current shortfalls of open source projects in inclusivity and diversity. In 2017 a GitHub open source survey found that 95% of respondents were male.

EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data

Publishing date: 2020-01-15 Published on: BMC Bioinformatics summary: This software article presents “https://github.com/MathOnco/EvoFreq">EvoFreq<, a comprehensive tool to visualise the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods.

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data

Publishing date: 2020-01-15 Published on: PLOS ONE summary: Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest such as disease state. A key challenge in this is the composition and dimensionality of microbiome data.

Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data

Publishing date: 2020-01-15 Published on: BMC Bioinformatics summary: None authors: Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li & Jia Gu link to paper: https://bmcbioinformatics.

ICE Contract With GitHub Sparks Developer Protests

Publishing date: 2020-01-15 Published on: The Atlantic summary: With 37 million users, GitHub is the largest host of source code in the world. Much of the code hosted on GitHub is open source, meaning it’s accessible, shareable, and modifiable to anyone.

NUFEB: A massively parallel simulator for individual-based modelling of microbial communities

Publishing date: 2020-01-15 Published on: PLOS Computational Biology summary: None authors: Bowen Li, Denis Taniguchi, Jayathilake Pahala Gedara, Valentina Gogulancea, Rebeca Gonzalez-Cabaleiro, Jinju Chen, Andrew Stephen McGough, Irina Dana Ofiteru, Thomas P.

PyLandStats: An open-source Pythonic library to compute landscape metrics

Publishing date: 2020-01-15 Published on: PLOS ONE summary: Channel Editor Summary: PyLandStats is a fantastic example of an open source scientific package, with an open licence (GPL), clear documentation for both users and developers, and a source code repository set up to easily enable contributions and bug reports.

Ten quick tips for delivering programming lessons

Publishing date: 2020-01-15 Published on: PLOS Computational Biology summary: Teaching well is a craft like any other, and success often comes from an accumulation of small improvements rather than from any single large change.

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software

Publishing date: 2019-11-14 Published on: Giga Science summary: The authors have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages.

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data

Publishing date: 2019-11-14 Published on: Genome Biology summary: Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. The authors present DeepImpute, a deep neural network-based imputation algorithm that uses dropout layers and loss functions to learn patterns in the data, allowing for accurate imputation.

Introducing Mozilla Open Leaders X

Publishing date: 2019-11-14 Published on: Mozilla Foundation summary: Here are the new, community-run Open Leaders programs with diverse audiences that serve as entry-points into the internet health movement. From September through November, these programs have gone through movement building training and program-design mentorship in preparation to launch their own Open Leaders program in 2020.

Measuring sustainability of seed-funded earth science informatics projects

Publishing date: 2019-11-14 Published on: PLOS ONE summary: Short term funding is a common funding model for informatics projects. Funders are interested in maximizing the sustainability and accessibility of the outputs, but there are no commonly accepted practices to do so in the Earth sciences informatics field.

odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments

Publishing date: 2019-11-14 Published on: Frontiers in Neuroinformatics summary: None authors: Julia Sprenger, Lyuba Zehl, Jana Pick, Michael Sonntag, Jan Grewe, Thomas Wachtler, Sonja Grün, and Michael Denker link to paper: https://doi.

Open Source Seed, a Revolution in Breeding or Yet Another Attack on the Breeder’s Exemption?

Publishing date: 2019-11-14 Published on: Frontiers in Plant Science summary: The Open Source Seed Initiative was initiated in 2012. Following concerns about the concentration in the seed sector and the rise of patenting, the initiative is “dedicated to maintaining fair and open access to plant genetic resources worldwide in order to ensure the availability of germplasm to farmers, gardeners, breeders, and communities of this and future generations.

Ramf: An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi

Publishing date: 2019-11-14 Published on: Frontiers in Plant Science summary: None authors: Marco Chiapello, Debatosh Das and Caroline Gutjahr link to paper: https://doi.org/10.3389/fpls.2019.01184 Icons made by catkuro from www.flaticon.com

The TargetMine Data Warehouse: Enhancement and Updates

Publishing date: 2019-11-14 Published on: Frontiers in Genetics summary: Biological data analysis is the key to new discoveries in disease biology and drug discovery. The rapid proliferation of high-throughput ‘omics’ data has necessitated a need for tools and platforms that allow the researchers to combine and analyse different types of biological data and obtain biologically relevant knowledge.

A story of hobbies and a hobby of stories

Publishing date: 2019-10-17 Published on: SCIENTISTNOBEE summary: None authors: SCIENTISTNOBEE link to paper: https://scientistnobee.wordpress.com/a-story-of-hobbies-and-a-hobby-of-stories/ Icons made by catkuro from www.flaticon.com

Agreement between the spatiotemporal gait parameters from two different wearable devices and high-speed video analysis

Publishing date: 2019-10-17 Published on: PLOS ONE summary: This study aimed to evaluate the concurrent validity of two different inertial measurement units for measuring spatiotemporal parameters during running on a treadmill, by comparing data with a high-speed video analysis (VA) at 1,000 Hz.

An Open Source Syringe Pump Controller for Fluid Delivery of Multiple Volumes

Publishing date: 2019-10-17 Published on: eNeuro summary: Syringe pumps are a necessary piece of laboratory equipment that are used for fluid delivery in behavioral neuroscience laboratories. Many experiments provide rodents and primates with fluid rewards such as juice, water, or liquid sucrose.

Free-space transfer of comb-rooted optical frequencies over an 18 km open-air link

Publishing date: 2019-10-17 Published on: Nature Communications summary: Phase-coherent transfer of optical frequencies over a long distance is required for diverse photonic applications, including optical clock dissemination and physical constants measurement.

Joint emulation of Earth System Model temperature-precipitation realizations with internal variability and space-time and cross-variable correlation: fldgen v2.0 software description

Publishing date: 2019-10-17 Published on: PLOS ONE summary: Earth System Models (ESMs) are excellent tools for quantifying many aspects of future climate dynamics but are too computationally expensive to produce large collections of scenarios for downstream users of ESM data.

ODX: A Fitness Tracker-Based Device for Continuous Bacterial Growth Monitoring

Publishing date: 2019-10-17 Published on: ACS Publications summary: None authors: Venkata V. B. YallapragadaUday GowdaDavid WongLiam O’FaolainMark TangneyGanga C. R. Devarapu link to paper: https://pubs.acs.org/doi/pdf/10.1021/acs.analchem.9b02628 Icons made by catkuro from www.

SignalBuddy

Publishing date: 2019-10-17 Published on: OpenBehavior summary: None authors: Richard Warren link to paper: http://edspace.american.edu/openbehavior/2019/09/19/signalbuddy/ Icons made by catkuro from www.flaticon.com

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

Publishing date: 2019-10-17 Published on: PLOS Computational Biology summary: Almost half of the human genome is composed of transposable elements (TEs), but their contribution to the transcriptome, their cell-type specific expression patterns, and their role in disease remains poorly understood.

The Open Know-How Manifest Specification

Publishing date: 2019-10-17 Published on: StandardsRepo summary: Open Know-How is all about sharing how to make things. With dozens of open hardware organisations and over 80 content-hosting platforms and thousands of designers sharing open hardware designs Open Know-How is making it easier to share and find documentation on how to make things and will reduce crossover/duplication of effort across sectors.

“My life after stroke through a camera lens”- A photovoice study on participation in Sweden

Publishing date: 2019-10-17 Published on: PLOS ONE summary: An increasing number of people with stroke live in their communities, yet the understanding of how their reintegration into society can best be facilitated is incomplete.

New methods of removing debris and high-throughput counting of cyst nematode eggs extracted from field soil

Publishing date: 2019-10-15 Published on: PLOS ONE summary: None authors: Upender Kalwa, Christopher Legner, Elizabeth Wlezien, Gregory Tylka, Santosh Pandey link to paper: 10.1371/journal.pone.0223386 Icons made by catkuro from www.flaticon.com

Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures

Publishing date: 2019-09-26 Published on: PLOS Biology summary: Methods for measuring the properties of individual cells within their native 3D environment will enable a deeper understanding of embryonic development, tissue regeneration, and tumorigenesis.

Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits

Publishing date: 2019-09-26 Published on: Neuron summary: Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease.

Open Source Tools and Methods

Publishing date: 2019-09-26 Published on: eNeuro summary: eNeuro announce a new type of paper to provide a venue to share open-source tools and methods. Introducing this new type of papers offers several advantages: reducing the time and money laboratories spend to reinvent methods; increasing transparency; and improving reproducibility.

Ten simple rules for helping newcomers become contributors to open projects

Publishing date: 2019-09-26 Published on: PLOS Computational Biology summary: Open source projects are nothing but a collaborative effort of community members. The constant involvement of maintainers, contributors, and users make open source software sustainable and keeps the community as a whole going.

uORF-Tools – Workflow for the determination of translation-regulatory upstream open reading frames

Publishing date: 2019-09-26 Published on: PLOS ONE summary: Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs.

Comparing record linkage software programs and algorithms using real-world data

Publishing date: 2019-09-24 Published on: PLOS ONE summary: None authors: Alan F. Karr, Matthew T. Taylor, Suzanne L. West, Soko Setoguchi, Tzuyung D. Kou, Tobias Gerhard, Daniel B. Horton link to paper: 10.

A 3D Printed Device for Low Cost Neural Stimulation in Mice

Publishing date: 2019-09-05 Published on: Frontiers Neuroscience summary: None authors: Taylor J. Morrison, Elana Sefton, Melissa Marquez-Chin, Milos R. Popovic, Cindi M. Morshead and Hani E. Naguib link to paper: https://www.

AMi: a GUI-based, open-source system for imaging samples in multi-well plates

Publishing date: 2019-09-05 Published on: Methods Communications summary: None authors: A. Bohm link to paper: http://scripts.iucr.org/cgi-bin/paper?S2053230X19009853 Icons made by catkuro from www.flaticon.com

High-speed device synchronization in optical microscopy with an open-source hardware control platform

Publishing date: 2019-09-05 Published on: Scientific Reports summary: High-speed synchronization of multiple devices is a necessity for modern optical microscopy techniques and this paper simplifies the process for those building custom microscope systems by providing a hardware control platform that reduces the need for custom software while expanding the scope of compatible peripheral devices.

Internet of Things Applied in Healthcare Based on Open Hardware with Low-Energy Consumption

Publishing date: 2019-09-05 Published on: Healthcare Informatics Research summary: The Internet of Things (IoT) and its applications are growing simultaneously. These applications need new intelligent devices along heterogeneous networking. Which makes them costly to implement indeed.

Leveraging conservation action with open‐source hardware

Publishing date: 2019-09-05 Published on: The Society for Conservation Biology summary: Data collection by conservation biologists is undergoing radical change, with researchers collaborating across disciplines to create bespoke, low‐cost monitoring equipment from open‐source hardware (OSH).

Nesting box imager: Contact-free, real-time measurement of activity, surface body temperature, and respiratory rate applied to hibernating mouse models

Publishing date: 2019-09-05 Published on: PLOS Biology summary: If you’re trying to measure animal activity without disturbing a hibernating animal your options were previously limited and expensive but the growing utility and shrinking price of sensors, cameras and single-board computers has enabled this device for monitoring mice nesting boxes using a Raspberry Pi and an infrared camera for under $400.

Facilitating reproducible project management and manuscript development in team science: The projects R package

Publishing date: 2019-08-16 Published on: PLOS ONE summary: The contemporary scientific community places a growing emphasis on the reproducibility of research. The projects R package is a free, open-source package created in the interest of facilitating reproducible research workflows.

How to support open-source software and stay sane

Publishing date: 2019-08-16 Published on: Nature Toolbox summary: Releasing lab-built open-source software often involves a mountain of unforeseen work for the developers. It’s a familiar problem: open-source software is widely acknowledged as crucially important in science, yet it is funded non-sustainably.

Open collaborative writing with Manubot

Publishing date: 2019-08-16 Published on: PLOS Computational Biology summary: Traditionally, scholarly manuscripts have been written in private by a predefined team of collaborators. But now the internet enables realtime open science, where project communication occurs online in a public venue and anyone is able to contribute.

Open Source Is Good, but How Can It Do Good?

Publishing date: 2019-08-16 Published on: Linux Journal summary: The Open Source world may not be so explicit about the underlying ethical aspect, but most coders probably would hope that their programming makes the world a better place.

Kankanet: An artificial neural network-based object detection smartphone application and mobile microscope as a point-of-care diagnostic aid for soil-transmitted helminthiases

Publishing date: 2019-08-05 Published on: PLOS Neglected Tropical Diseases summary: None authors: Ariel Yang, Nahid Bakhtari, Liana Langdon-Embry, Emile Redwood, Simon Grandjean Lapierre, Patricia Rakotomanga, Armand Rafalimanantsoa, Juan De Dios Santos, Inès Vigan-Womas, Astrid M.

Low-cost solution for rodent home-cage behaviour monitoring

Publishing date: 2019-08-02 Published on: PLOS ONE summary: None authors: Surjeet Singh, Edgar Bermudez-Contreras, Mojtaba Nazari, Robert J. Sutherland, Majid H. Mohajerani link to paper: 10.1371/journal.pone.0220751 Icons made by catkuro from www.

3D μ F - Interactive Design Environment for Continuous Flow Microfluidic Devices

Publishing date: 2019-07-29 Published on: Scientific Reports summary: In this paper, the authors present an interactive tool for designing continuous flow microfluidic devices. 3DμF is the first completely open source interactive microfluidic system designer that readily supports state of the art design automation algorithms.

Harnessing robotic automation and web-based technologies to modernize scientific outreach

Publishing date: 2019-07-29 Published on: PLOS Biology summary: Technological breakthroughs in the past two decades have ushered in a new era of biomedical research, turning it into an information-rich and technology-driven science.

Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues

Publishing date: 2019-07-29 Published on: Nature Communications summary: Recent advances in optical clearing and light-sheet microscopy have provided unprecedented access to structural and molecular information from intact tissues. However, current light-sheet microscopes have imposed constraints on the size, shape, number of specimens, and compatibility with various clearing protocols.

On the Economic Value of Open Source Hardware – Case Study of an Open Source Magnetic Resonance Imaging Scanner

Publishing date: 2019-07-29 Published on: Journal of Open Hardware summary: Increasing maturation and dissemination of easy-to-use and affordable means of digital production (e.g. 3D printing), access to these in makerspaces and FabLabs as well as powerful tools and online platforms for virtual and collaborative product design enabled the highly efficient and innovative mode of open source to spill over from software to hardware.

Open Hardware: Open-Source MRI Scanners Could Bring Enormous Cost Savings

Publishing date: 2019-07-29 Published on: 3DPrint.com summary: None authors: Bridget O’Neal link to paper: https://3dprint.com/247312/researchers-discuss-potential-open-source-mris-enormous-savings-cost/ Icons made by catkuro from www.flaticon.com

Open(G)PIAS: An Open-Source Solution for the Construction of a High-Precision Acoustic Startle Response Setup for Tinnitus Screening and Threshold Estimation in Rodents

Publishing date: 2019-07-29 Published on: Frontiers in Behavioral Neuroscience summary: None authors: Richard Gerum, Hinrich Rahlfs, Matthias Streb, Patrick Krauss, Jannik Grimm, Claus Metzner, Konstantin Tziridis, Michael Günther, Holger Schulze, Walter Kellermann and Achim Schilling

Rodent Activity Detector (RAD), an Open Source Device for Measuring Activity in Rodent Home Cages

Publishing date: 2019-07-29 Published on: eNeuro summary: None authors: Bridget A. Matikainen-Ankney, Marcial Garmendia-Cedillos, Mohamed Ali, Jonathan Krynitsky, Ghadi Salem, Nanami L. Miyazaki, Tom Pohida and Alexxai V. Kravitz link to paper: https://www.

Scientific Community Image Forum: A discussion forum for scientific image software

Publishing date: 2019-07-04 Published on: PLOS Biology summary: Channel Editor Summary: In open source software, open code and free software is only the tip of the iceberg. Successful open source projects tend to have strong communities supporting both contributors as well as users - but this often comes with the hidden cost in volunteer (or staff) time and resources.

The WIRED Guide to Open Source Software

Publishing date: 2019-07-04 Published on: WIRED summary: Now open source is practically everywhere. Walmart uses open source software like the development platform Node, and it has opened up the code of its cloud management tool OneOps and its development platform Electrode.

Tungsten filled 3D printed field shaping devices for electron beam radiation therapy

Publishing date: 2019-06-19 Published on: PLOS ONE summary: None authors: Lawrie Skinner, Benjamin P. Fahimian, Amy S. Yu link to paper: 10.1371/journal.pone.0217757 Icons made by catkuro from www.flaticon.com

A 3D-printed hand-powered centrifuge for molecular biology

Publishing date: 2019-06-17 Published on: PLOS Biology summary: None authors: Gaurav Byagathvalli, Aaron Pomerantz, Soham Sinha, Janet Standeven, M. Saad Bhamla link to paper: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000251 Icons made by catkuro from www.

An improved liquid–liquid separator based on an optically monitored porous capillary

Publishing date: 2019-06-17 Published on: Reaction Chemistry & Engineering summary: Channel Editor Summary: The authors report on an open hardware separator for immiscible liquids like oil and water using porous tubing and a number of off-the-shelf components or DIY parts.

Automation of fizzy extraction enabled by inexpensive open-source modules

Publishing date: 2019-06-17 Published on: Heliyon summary: Channel Editor Summary: This paper by Yang, Chang and Urban presents an automated system for preparing and analysing chemical components using fizzy extraction. Based on Arduino and other breakout boards, the system can be integrated to commercially available mass spectrometers, and outputs data in digital, as well as printed format.

Incu-Stream 1.0: An Open-Hardware Live-Cell Imaging System Based on Inverted Bright-Field Microscopy and Automated Mechanical Scanning for Real-Time and Long-Term Imaging of Microplates in Incubator

Publishing date: 2019-06-17 Published on: IEEE Access summary: Channel Editor Summary: The authors present a microplate-compatible inverted bright-field microscope system that can be used inside incubators to monitor cell growth in real-time and under controlled conditions.

Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware

Publishing date: 2019-06-17 Published on: Scientific Reports summary: None authors: Tomas Aidukas, Regina Eckert, Andrew R. Harvey, Laura Waller & Pavan C. Konda link to paper: https://www.nature.com/articles/s41598-019-43845-9 Icons made by catkuro from www.

OSA | Open-source do-it-yourself multi-color fluorescence smartphone microscopy

Publishing date: 2019-06-17 Published on: Biomedical Optics Express summary: None authors: Yulung Sung, Fernando Campa, and Wei-Chuan Shih link to paper: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-8-11-5075 Icons made by catkuro from www.flaticon.com

UV Transilluminators and Imaging on the Cheap

Publishing date: 2019-06-17 Published on: Lab On The Cheap summary: Lab On The Cheap have"http://www.labonthecheap.com/index.php/2018/04/10/technical-tuesday-economical-electrophoresis/"> written about Gel Electrophoresis before<, the punchline of which was that “https://www.minipcr.com/product/bluegel-electrophoresis-with-built-in-illuminator/">MiniPCR has good gel electrophoresis and imaging system for just $350<.

Low-cost (<€5), open-source, potential alternative to commercial spectrophotometers

Publishing date: 2019-06-12 Published on: PLOS Biology summary: None authors: Vasco Ribeiro Pereira, Bill Stephen Hosker link to paper: 10.1371/journal.pbio.3000321 Icons made by catkuro from www.flaticon.com

ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data

Publishing date: 2019-06-04 Published on: PLOS ONE summary: Single-molecule fluorescence microscopy studies of bacteria provide unique insights into the mechanisms of cellular processes and protein machineries in ways that are unrivalled by any other technique.

Dstl shares new open-source framework initiative

Publishing date: 2019-05-23 Published on: GOV.UK summary: A new open-source software framework designed by the Defence Science and Technology Laboratory (Dstl) is now available to help improve tracking technology. Leading the project across the 5-eyes nations of UK, USA, Australia, NZ and Canada, Dstl has made the project available to anyone wanting to upload and test their tracking algorithms.

Essential Open Source Software for Science

Publishing date: 2019-05-23 Published on: Chan Zuckerberg Science Initiative summary: Chan Zuckerberg Foundation design a new program to support open source software essential to modern scientific research. The Chan Zuckerberg Initiative will soon invite applications for open source software projects that are essential to biomedical research.

Machine learning to help researchers evaluate biases in clinical trials: a prospective, randomized user study

Publishing date: 2019-05-23 Published on: BMC Medical Informatics and Decision Making summary: Assessing risks of bias in randomized controlled trials (RCTs) is an important but laborious task when conducting systematic reviews.

Reproducible big data science: A case study in continuous FAIRness

Publishing date: 2019-05-23 Published on: PLOS ONE summary: In recent years, researchers have access to larger volumes of data. More and more hypotheses are now developed and tested against existing data rather than by generating new data.

Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments

Publishing date: 2019-05-23 Published on: PLOS Computational Biology summary: This paper presents Stytra, a flexible, open-source software package, written in Python and designed to cover all the general requirements involved in larval zebrafish behavioral experiments.

3D-printable portable open-source platform for low-cost lens-less holographic cellular imaging

Publishing date: 2019-05-02 Published on: arXiv summary: None authors: Stephan Amann, Max von Witzleben, Stefan Breuer link to paper: https://arxiv.org/pdf/1904.04497.pdf Icons made by catkuro from www.flaticon.com

Automating multimodal microscopy with NanoJ-Fluidics

Publishing date: 2019-05-02 Published on: Nature Communications summary: Channel Editor Summary: The authors have developed an open source and low-cost device for automated control of labelling and washing cells while under the microscope.

IntensityCheck – The light measuring app for microscope performance checks and consistent fluorescence imaging

Publishing date: 2019-05-02 Published on: PLOS ONE summary: Quantitative fluorescence imaging is an essential tool in biomedical research. It requires consistent and repeatable conditions such as constant sample illumination. Even on a confocal microscope this can usually only be achieved by using an external laser power meter.

BioModelos: A collaborative online system to map species distributions

Publishing date: 2019-04-11 Published on: PLOS ONE summary: Information on species distribution is recognized as a crucial input for biodiversity conservation and management. To that end, considerable resources have been dedicated towards increasing the quantity and availability of species occurrence data, boosting their use in species distribution modeling and online platforms for their dissemination.

Community-led data collection using Open Data Kit for surveillance of animal African trypanosomiasis in Shimba hills, Kenya

Publishing date: 2019-04-11 Published on: BMC Research Notes summary: In Sub-Saharan Africa, there is an increase in trypanosome non-susceptibility to multiple trypanocides, but limited information on judicious trypanocide use is accessible to smallholder farmers and agricultural stakeholders in disease endemic regions, resulting in widespread multi-drug resistance.

ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

Publishing date: 2019-04-11 Published on: PLOS Computational Biology summary: Interacting-particle reaction dynamics (iPRD) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction kinetics, in which particles appear, disappear, or change their type and interactions based on a set of reaction rules.

RMut: R package for a Boolean sensitivity analysis against various types of mutations

Publishing date: 2019-04-11 Published on: PLOS ONE summary: There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones.

RUPEE: A fast and accurate purely geometric protein structure search

Publishing date: 2019-04-11 Published on: PLOS ONE summary: Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results.

The Shift From Open Source To Commercial Data Analytics Is Placing Cost Over Accuracy

Publishing date: 2019-04-11 Published on: Forbes summary: The modern era of data science was once built upon an open and transparent world of open source software and open data, wielded by statistically literate technical experts who deeply understood both the tools and data they were using.

The Turing Way

Publishing date: 2019-04-11 Published on: The Turing Way summary: The Turing Way is a lightly opinionated guide to reproducible data science. The goal of The Turing Way is to provide all the information that researchers need at the start of their projects to ensure that they are easy to reproduce at the end.

CLEESE: An open-source audio-transformation toolbox for data-driven experiments in speech and music cognition

Publishing date: 2019-04-04 Published on: PLOS ONE summary: None authors: Juan José Burred, Emmanuel Ponsot, Louise Goupil, Marco Liuni, Jean-Julien Aucouturier link to paper: 10.1371/journal.pone.0205943 Icons made by catkuro from www.

Design and basic research on accuracy of a novel individualized three-dimensional printed navigation template in atlantoaxial pedicle screw placement

Publishing date: 2019-04-02 Published on: PLOS ONE summary: None authors: Xiao-Long Chen, Ya-Fen Xie, Jian-Xin Li, Wu Wu, Guan-Nan Li, Hui-Jing Hu, Xiao-Yun Wang, Zhao-Jian Meng, Yue-Feng Wen, Wen-Hua Huang

Deploying Acoustic Detection Algorithms on Low-Cost, Open-Source Acoustic Sensors for Environmental Monitoring

Publishing date: 2019-03-28 Published on: Sensors summary: Conservation researchers require low-cost access to acoustic monitoring technology. However, affordable tools are often constrained to short-term studies due to high energy consumption and limited storage.

AutonoMouse: High throughput operant conditioning reveals progressive impairment with graded olfactory bulb lesions

Publishing date: 2019-03-28 Published on: PLOS ONE summary: None authors: Andrew Erskine, Thorsten Bus, Jan T. Herb, Andreas T. Schaefer link to paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0211571 Icons made by catkuro from www.flaticon.com

Developing and adopting safe and effective digital biomarkers to improve patient outcomes

Publishing date: 2019-03-28 Published on: npj Digital Medicine summary: Biomarkers are physiologic, pathologic, or anatomic characteristics that are objectively measured and evaluated as an indicator of normal biologic processes, pathologic processes, or biological responses to therapeutic interventions.

Glucose biosensor based on open-source wireless microfluidic potentiostat

Publishing date: 2019-03-28 Published on: Sensors and Actuators B: Chemical summary: Wireless potentiostats capable of cyclic voltammetry and amperometry that connect to the Internet are emerging as key attributes of future point-of-care devices.

pyPhotometry: Open source Python based hardware and software for fiber photometry data acquisition

Publishing date: 2019-03-28 Published on: Scientific Reports summary: Channel Editor Summary: Fiber photometry allows researchers to record neural activity by measuring changes in fluorescence of chemical indicators using an optical fibre and is a powerful technique that is currently quite expensive to perform.

Sample treatment platform for automated integration of microextraction techniques and liquid chromatography analysis

Publishing date: 2019-03-28 Published on: HardwareX summary: Sample preparation performance influences the quality of every chemical analysis. Since it is the most labor-intensive stage in the nearly all-analytical protocols, sample preparation automation would be desirable, to increase the analytical throughput, maintaining precision and accuracy, while preventing risks of human exposure to chemical or biological agents.

PhyloPi: An affordable, purpose built phylogenetic pipeline for the HIV drug resistance testing facility

Publishing date: 2019-03-05 Published on: PLOS ONE summary: None authors: Phillip Armand Bester, Andrie De Vries, Stephanus Riekert, Kim Steegen, Gert van Zyl, Dominique Goedhals link to paper: 10.1371/journal.pone.0213241 Icons made by catkuro from www.

Apollo: Democratizing genome annotation

Publishing date: 2019-02-27 Published on: PLOS Computational Biology summary: Genome annotation is the process of identifying the location and function of a genome’s encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms.

BioJava 5: A community driven open-source bioinformatics library

Publishing date: 2019-02-27 Published on: PLOS Computational Biology summary: Channel Editor Summary: BioJava is an open source project which provides a Java framework for processing biological data. The project offers analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures.

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA

Publishing date: 2019-02-27 Published on: PLOS ONE summary: The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data.

Open Science Means Open Source–Or, at Least, It Should

Publishing date: 2019-02-27 Published on: Linux Journal summary: When did open source begin? In February 1998, when the term was coined by Christine Peterson? Or in 1989, when Richard Stallman drew up the “subroutinized” GNU GPL?

Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation

Publishing date: 2019-02-01 Published on: PLOS Biology summary: Channel Editor Summary: Open-source, scalable and high-throughput protocols for purifying DNA and RNA using magnetic beads are presented, providing easy to use methods for some of the most common processes in molecular biology.

Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example

Publishing date: 2019-02-01 Published on: bioRxiv summary: None authors: A. Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter link to paper: https://www.biorxiv.org/content/10.1101/521096v1 Icons made by catkuro from www.

Expanding Equitable Access to Experimental Research and STEM Education by Supporting Open Source Hardware Development

Publishing date: 2019-02-01 Published on: Journal of Open HW summary: Is there an opportunity to radically increase access to scientific instrumentation, while improving the quality and diversity of research tools by harnessing the power of collaborative innovation in the development of FOSH (free and open source hardware)?

Open sourcing bioinstruments

Publishing date: 2019-02-01 Published on: Bits of DNA summary: While open sourcing has become de rigueur in genomics dry labs, wet labs remain beholden to commercial instrument providers that rarely open source hardware or software, and impose draconian restrictions on instrument use and modification.

Open-source automated chemical vapor deposition system for the production of two- dimensional nanomaterials

Publishing date: 2019-02-01 Published on: PLOS ONE summary: The study of two- dimensional (2D) materials is a rapidly growing area within nanomaterials research. However, the high equipment costs, which include the processing systems necessary for creating these materials, can be a barrier to entry for some researchers interested in studying these novel materials.

Open-Source Multiparametric Optocardiography

Publishing date: 2019-02-01 Published on: Scientific Reports summary: None authors: None link to paper: https://www.nature.com/articles/s41598-018-36809-y Icons made by catkuro from www.flaticon.com

optoPAD: a closed-loop optogenetics system to study the circuit basis of feeding behaviors

Publishing date: 2019-02-01 Published on: bioRxiv summary: The regulation of feeding plays a key role in determining the fitness of animals through its impact on nutrition. Elucidating the circuit basis of feeding and related behaviors is an important goal in neuroscience.

VasoTracker, a low-cost and open source pressure myograph system for vascular physiology

Publishing date: 2019-02-01 Published on: Physiology | Frontiers summary: None authors: Penelope F. Lawton, Matthew D. Lee, Christopher D. Saunter, John M. Girkin1, John G. McCarron and Calum Wilson link to paper: https://www.

Bayesian multiple logistic regression for case-control GWAS

Publishing date: 2019-01-17 Published on: PLOS Genetics summary: Genetic variants in genome-wide association studies (GWAS) are tested for disease association mostly using simple regression, one variant at a time. Standard approaches to improve power in detecting disease-associated SNPs use multiple regression with Bayesian variable selection in which a sparsity-enforcing prior on effect sizes is used to avoid overtraining and all effect sizes are integrated out for posterior inference.

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens

Publishing date: 2019-01-17 Published on: PLOS Computational Biology summary: Channel Editor’s Summary: To many, open source software means “free to use”, and to others it might mean “I can see and re-use the code freely”.

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

Publishing date: 2019-01-17 Published on: PLOS Biology summary: A personalized approach based on a patient’s or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles.

Julia language co-creators win James H. Wilkinson Prize for Numerical Software

Publishing date: 2019-01-17 Published on: MIT News summary: Three co-creators of the MIT-incubated Julia programming language are the recipients of the 2019 James H. Wilkinson Prize for Numerical Software. The prize will be awarded to Bezanson, Karpinski, and Shah “for the creation of Julia, an innovative environment for the creation of high-performance tools that enable the analysis and solution of computational science problems.

Validating quantum-classical programming models with tensor network simulations

Publishing date: 2019-01-17 Published on: PLOS ONE summary: The exploration of hybrid quantum-classical algorithms and programming models on noisy near-term quantum hardware has begun. As hybrid programs scale towards classical intractability, validation and benchmarking are critical to understanding the utility of the hybrid computational model.

Cell colony counter called CoCoNut

Publishing date: 2018-12-20 Published on: PLOS ONE summary: CoCoNut removes the need for slow and eye-straining manual counting of viable colonies under a microscope. It’s a semi-automated, image-based cell colony counting setup that combines 3D-printed hardware and an ImageJ plugin.

Open-source sensor for measuring oxygen partial pressures below 100 microbars

Publishing date: 2018-12-20 Published on: PLOS ONE summary: This nifty device measures partial pressure of oxygen in a similar manner to commercial devices, yet at substantially reduced cost. In a nutshell, a sinusoidally modulated LED excites a luminescent dye over time, while a photodiode picks up the spectrally shifted emission light from the dye.

A large-scale analysis of bioinformatics code on GitHub

Publishing date: 2018-12-10 Published on: PLOS ONE summary: In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software.

An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes

Publishing date: 2018-12-10 Published on: PLOS ONE summary: The classification of infections is a routine component of clinical management. Kameris is an open source toolkit for a supervised and alignment-free subtyping method which operates on HIV-1 sequences.

Assessing a novel way to measure step count while walking using a custom mobile phone application

Publishing date: 2018-12-10 Published on: PLOS ONE summary: Walking speed has been associated with many clinical outcomes (e.g., frailty, mortality, joint replacement need, etc.). Accurately measuring walking speed (stride length x step count/time) typically requires significant clinician/staff time or a gait lab with specialized equipment (i.

Feeling generous? Open source software community gives shelter to code

Publishing date: 2018-12-10 Published on: JAXENTER summary: Are you looking for a new project to work on? Do you have some code that you’d like to donate? In this piece, Sarah Schlothauer presents a shortlist of free and open source communities dedicated to the world of FOSS.

Is Open Source Project Participation Worthwhile?

Publishing date: 2018-12-10 Published on: Forbes summary: Matthew Barlocker is the Founder and CEO of AWS monitoring software startup “Blue Matador”, and discusses here the specific benefits of contributing to an open source project.

Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus

Publishing date: 2018-12-10 Published on: PLOS NEGLECTED TROPICAL DISEASES summary: Although the plaque reduction neutralization test (PRNT) is an important assay for measuring neutralizing antibody responses against many viruses, no free, open-source programs specifically designed for virus plaque counting and neutralizing antibody titer estimation are available.

Design and validation of an open-source modular Microplate Photoirradiation System for high-throughput photobiology experiments

Publishing date: 2018-11-19 Published on: PLOS ONE summary: This paper presents a useful open-source Microplate Photoirradiation System (MPS) for use in standard 96- and 24-well microplates that allows photobiologists to conduct a variety of experiments in a high-throughput format, inlcuding inside incubators.

Spikeling: A low-cost hardware implementation of a spiking neuron for neuroscience teaching and outreach

Publishing date: 2018-11-19 Published on: PLOS Biology summary: Spikeling provides an in silico model of a spiking neuron that can be used to illustrate their biophysical behaviour through sound and light inputs and outputs as well as a custom oscilloscope interface.

GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components

Publishing date: 2018-10-23 Published on: PLOS ONE summary: This paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development.

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays

Publishing date: 2018-10-23 Published on: PLOS Computational Biology summary: In this paper, Gelfman et al. present an open-source R package ‘meaRtools’ that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs).

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor

Publishing date: 2018-10-23 Published on: PLOS Computational Biology summary: Whilst many open source projects enter the spotlight as trend-setting new software packages, it’s nice to appreciate some of the long-lived projects as well.

A low-cost do-it-yourself microscope kit for hands-on science education

Publishing date: 2018-10-01 Published on: SPIE Digital Library summary: A low cost microscope kit “the other way round”: instead of requiring the user to peer through eye-pieces, this design aligns a series of lenses around a sample plane and shines light through the centre to project the greatly magnified image onto a piece of paper that can be comfortably observed with the naked eye.

Adapting open-source drone autopilots for real-time iceberg observations

Publishing date: 2018-10-01 Published on: MethodsX summary: In a nice example of adapting an existing tool, Daniel F.Carlson and Søren Rysgaard used OS control boards for Drones and its respective software as dataloggers to measure Iceberg characteristics (eg movement speed, orientation over time).

Approaches to Open Source 3-D Printable Probe Positioners and Micromanipulators for Probe Stations

Publishing date: 2018-10-01 Published on: HardwareX summary: This review of micromanipulator designs from Iiro Hietanen et al puts three open source alternatives through their paces with rigorous experimental testing, and explains the trade-off and decisions in weighing up cost and precision.

Open source capillary electrophoresis

Publishing date: 2018-10-01 Published on: Electrophoresis summary: Open source paradigm is becoming widely accepted in scientific communities and open source hardware is finding its steady place in chemistry research. In this review article, Petr Kubáň et al provide the reader with the most up‐to‐date information on open source hardware and software resources enabling the construction and utilization of an “open source capillary electrophoresis instrument”.

Haves and have nots must find a better way: The case for open scientific hardware

Publishing date: 2018-09-27 Published on: PLOS Biology summary: Many efforts are making science more open and accessible; they are mostly concentrated on issues that appear before and after experiments are performed: open access journals, open databases, and many other tools to increase reproducibility of science and access to information.

Testing for physical validity in molecular simulations

Publishing date: 2018-09-06 Published on: PLOS ONE summary: None authors: Pascal T. Merz, Michael R. Shirts link to paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202764 Icons made by catkuro from www.flaticon.com

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization

Publishing date: 2018-08-17 Published on: PLOS Computational Biology summary: Garrido-Martín et al. present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software.

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Publishing date: 2018-08-13 Published on: PLOS Computational Biology summary: None authors: None link to paper: http://dx.doi.org/10.1371/journal.pcbi.1006169 Icons made by catkuro from www.flaticon.com

Digital open science—Teaching digital tools for reproducible and transparent research

Publishing date: 2018-07-26 Published on: PLOS Biology summary: An important hallmark of science is the transparency and reproducibility of scientific results. Over the last few years, internet-based technologies have emerged that allow for a representation of the scientific process that goes far beyond traditional methods and analysis descriptions.

OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement

Publishing date: 2018-07-26 Published on: PLOS Computational Biology summary: Movement is fundamental to human and animal life, emerging through interaction of complex neural, muscular, and skeletal systems. Study of movement draws from and contributes to diverse fields, including biology, neuroscience, mechanics, and robotics.

PyPhi: A toolbox for integrated information theory

Publishing date: 2018-07-26 Published on: PLOS Computational Biology summary: Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, the authors introduce PyPhi, a Python software package that implements this framework for causal analysis and unfolds the full cause-effect structure of discrete dynamical systems of binary elements.

PSoC-Stat: A single chip open source potentiostat based on a Programmable System on a Chip

Publishing date: 2018-07-25 Published on: PLOS ONE summary: The potentiostat presented here from Prattana Lopin and Kyle V. Lopin can measure the presence of chemicals including vitamin C and lead without any external electronic components.

Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization

Publishing date: 2018-07-17 Published on: PLOS ONE summary: None authors: None link to paper: http://dx.doi.org/10.1371/journal.pone.0199771 Icons made by catkuro from www.flaticon.com

OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer

Publishing date: 2018-07-11 Published on: PLOS ONE summary: The accurate quantification of cellular and mitochondrial bioenergetic activity is of great interest in medicine and biology. This study provides statistical good practices to support experimentalists in designing, analyzing, testing, and reporting the results of mitochondrial stress tests using this high throughput platform.

Shedding Light: A New Open Source Imaging System

Publishing date: 2018-07-04 Published on: PLOS Research News summary: An interview with Isaac Nuñez and Tamara Matute, authors of the research article that was awarded the 2018 PLOS Open Source Toolkit Channel Prize.

CellProfiler 3.0: Next-generation image processing for biology

Publishing date: 2018-07-03 Published on: PLOS Biology summary: CellProfiler is a free software that has enabled researchers, without training in computer vision or programming community to create flexible, modular image analysis pipelines since its release in 2005.

Why open source isn’t just about code

Publishing date: 2018-06-01 Published on: TechRepublic summary: Abby Cabunoc Mayes of the Mozilla Foundation explains why open source is about culture as much as it is about code. authors: Dan Patterson & Abby Cabunoc Mayes

Efficient methods and readily customizable libraries for managing complexity of large networks

Publishing date: 2018-05-29 Published on: PLOS ONE summary: One common problem in visualizing real-life networks, including biological pathways, is the large size of these networks. Often times, users find themselves facing slow, non-scaling operations due to network size, if not a “hairball” network, hindering effective analysis.

Open-source micro-tensile testers via additive manufacturing for the mechanical characterization of thin films and papers

Publishing date: 2018-05-29 Published on: PLOS ONE summary: None authors: Krishanu Nandy, David W. Collinson, Charlie M. Scheftic, L. Catherine Brinson link to paper: 10.1371/journal.pone.0197999 Icons made by catkuro from www.

Ciw: An open-source discrete event simulation library

Publishing date: 2018-05-20 Published on: Journal of Simulation summary: This paper introduces Ciw, an open-source library for conducting discrete event simulations that has been developed in Python. The strengths of the library are illustrated in terms of best practice and reproducibility for computational research.

PlasmoTron: Semi-automated culture of malaria parasites

Publishing date: 2018-05-15 Published on: plasmotron.org summary: PlasmoTron is an open-source robotic system built on top of the OpenTrons platform, to allow semi-automated culture of malaria parasites. authors: Theo Sanderson and Julian C.

Porcupine: A visual pipeline tool for neuroimaging analysis

Publishing date: 2018-05-10 Published on: PLOS Computational Biology summary: The field of neuroimaging is rapidly adopting a more reproducible approach to data acquisition and analysis. Data structures and formats are being standardised and data analyses are getting more automated.

Mozilla’s 48-Hour Hackathon for a Better Internet

Publishing date: 2018-05-07 Published on: medium.com summary: Mozilla’s fifth-annual Global Sprint is May 10 and 11. Open-source engineers and activists around the globe will swap code and ideas to make the internet a healthier place.

If sharing is caring, Addgene really cares about plasmids.

Publishing date: 2018-05-05 Published on: PLOS Synbio Community summary: An interview with Addgene co-founder and current Chief Scientific Officer, Melina Fan. authors: Aaron Dy link to paper: http://blogs.plos.org/synbio/2016/05/05/if-sharing-is-caring-addgene-really-cares-about-plasmids/ Icons made by catkuro from www.

Bayesian reconstruction of transmission within outbreaks using genomic variants

Publishing date: 2018-04-18 Published on: PLOS Computational Biology summary: Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission.

Stop Hiding Your Code

Publishing date: 2018-04-18 Published on: PLOS Blogs Network summary: Difficulties reproducing scientific results are, in the vast majority of cases, not due to the authors having made mistakes or, even worse, forged data, writes Peter Wittek.

A ‘smart’ tube holder enables real-time sample monitoring in a standard lab centrifuge

Publishing date: 2018-04-16 Published on: PLOS ONE summary: In order to measure what happens to samples while being centrifuged, the authors created an adaptor that combines electronics and 3D printed parts to measure in real time how concentration changes along a tube containing samples, allowing protocol optimization.

Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy

Publishing date: 2018-04-13 Published on: PLOS Computational Biology summary: Modern microscopes allow us to acquire high quality external images of biological specimens, however, these can only be obtained at the very surface of the specimen.

pyBadlands: A framework to simulate sediment transport, landscape dynamics and basin stratigraphic evolution through space and time

Publishing date: 2018-04-12 Published on: PLOS ONE summary: Understanding Earth surface responses in terms of sediment dynamics to climatic variability and tectonics forcing is hindered by limited ability of current models to simulate long-term evolution of sediment transfer and associated morphological changes.

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems

Publishing date: 2018-04-11 Published on: PLOS Computational Biology summary: Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment.

webpic: A flexible web application for collecting distance and count measurements from images

Publishing date: 2018-04-02 Published on: PLOS ONE summary: Despite increasing ability to store and analyze large amounts of data for organismal and ecological studies, the process of collecting distance and count measurements from images has largely remained time consuming and error-prone, particularly for tasks for which automation is difficult or impossible.

Accessing microfluidics through feature-based design software for 3D printing

Publishing date: 2018-03-29 Published on: PLOS ONE summary: None authors: Peter G. Shankles, Larry J. Millet, Jayde A. Aufrecht, Scott T. Retterer link to paper: 10.1371/journal.pone.0192752 Icons made by catkuro from www.

The influence of transcript assembly on the proteogenomics discovery of microproteins

Publishing date: 2018-03-27 Published on: PLOS ONE summary: None authors: Jiao Ma, Alan Saghatelian, Maxim Nikolaievich Shokhirev link to paper: 10.1371/journal.pone.0194518 Icons made by catkuro from www.flaticon.com

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules

Publishing date: 2018-03-23 Published on: PLOS Computational Biology summary: None authors: Albert Solernou, Benjamin S. Hanson, Robin A. Richardson, Robert Welch, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris

Clinical value of patient-specific three-dimensional printing of congenital heart disease: Quantitative and qualitative assessments

Publishing date: 2018-03-21 Published on: PLOS ONE summary: Objective: Current diagnostic assessment tools remain suboptimal in demonstrating complex morphology of congenital heart disease (CHD). This limitation has posed several challenges in preoperative planning, communication in medical practice, and medical education.

Physical modeling of vortical cross-step flow in the American paddlefish, Polyodon spathula

Publishing date: 2018-03-21 Published on: PLOS ONE summary: None authors: Hannah Brooks, Grant E. Haines, M. Carly Lin, S. Laurie Sanderson link to paper: 10.1371/journal.pone.0193874 Icons made by catkuro from www.

Determinants of quality, latency, and amount of Stack Overflow answers about recent Android APIs

Publishing date: 2018-03-16 Published on: PLOS ONE summary: None authors: David Kavaler, Vladimir Filkov link to paper: 10.1371/journal.pone.0194139 Icons made by catkuro from www.flaticon.com

A modular, open-source, slide-scanning microscope for diagnostic applications in resource-constrained settings

Publishing date: 2018-03-15 Published on: PLOS ONE summary: Lu et al’s modular, open source, and fully automated slide-scanning microscope significantly reduces the cost and ease of use of whole slide imaging of diagnostic samples.

An empirical analysis of journal policy effectiveness for computational reproducibility

Publishing date: 2018-03-13 Published on: PNAS summary: A key component of scientific communication is sufficient information for other researchers in the field to reproduce published findings. For computational and data-enabled research, this has often been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters.

Build Hope – 2018 Hackaday Prize

Publishing date: 2018-03-13 Published on: Hackaday.io summary: The Hackaday Prize is the Academy Awards of Open Hardware, a grand competition where thousands of hardware hackers, makers and artists compete to build a better future.

PRISM: An open source framework for the interactive design of GPU volume rendering shaders

Publishing date: 2018-03-13 Published on: PLOS ONE summary: None authors: Simon Drouin, D. Louis Collins link to paper: 10.1371/journal.pone.0193636 Icons made by catkuro from www.flaticon.com

Assessing local resilience to typhoon disasters: A case study in Nansha, Guangzhou

Publishing date: 2018-03-09 Published on: PLOS ONE summary: None authors: Jinglu Song, Bo Huang, Rongrong Li link to paper: 10.1371/journal.pone.0190701 Icons made by catkuro from www.flaticon.com

ABrox—A user-friendly Python module for approximate Bayesian computation with a focus on model comparison

Publishing date: 2018-03-08 Published on: PLOS ONE summary: None authors: Ulf Kai Mertens, Andreas Voss, Stefan Radev link to paper: 10.1371/journal.pone.0193981 Icons made by catkuro from www.flaticon.com

Bat detective—Deep learning tools for bat acoustic signal detection

Publishing date: 2018-03-08 Published on: PLOS Computational Biology summary: None authors: Oisin Mac Aodha, Rory Gibb, Kate E. Barlow, Ella Browning, Michael Firman, Robin Freeman, Briana Harder, Libby Kinsey, Gary R.

Do-It-Yourself reliable pH-stat device by using open-source software, inexpensive hardware and available laboratory equipment

Publishing date: 2018-03-06 Published on: PLOS ONE summary: Milanovic et al present the construction of a reliable and inexpensive pH stat device allowing closed loop monitoring and control of pH using open-source, low-cost and/or readily available laboratory devices.

StimDuino: An Arduino-based electrophysiological stimulus isolator

Publishing date: 2018-03-01 Published on: Journal of Neuroscience Methods summary: Electrical stimulus isolator is a widely used device in electrophysiology. The timing of the stimulus application is usually automated and controlled by the external device or acquisition software; however, the intensity of the stimulus is adjusted manually.

Ten simple rules for collaborative lesson development

Publishing date: 2018-03-01 Published on: PLOS Computational Biology summary: Lessons take significant effort to build and even more to maintain. Most academics do this work on their own, but leveraging a community approach can make educational resource development more sustainable, robust, and responsive.

The Code and Data Citation Counter

Publishing date: 2018-03-01 Published on: github.com summary: Allow researchers and policy makers to see how the presence and quality of links to data and software in publications are changing over time so that they can identify emergent behaviour.

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries

Publishing date: 2018-02-23 Published on: PLOS ONE summary: None authors: Steven Shave, Stefan Mann, Joanna Koszela, Alastair Kerr, Manfred Auer link to paper: 10.1371/journal.pone.0193332 Icons made by catkuro from www.flaticon.com

Design of a 3D-printed, open-source wrist-driven orthosis for individuals with spinal cord injury

Publishing date: 2018-02-22 Published on: PLOS ONE summary: None authors: Alexandra A. Portnova, Gaurav Mukherjee, Keshia M. Peters, Ann Yamane, Katherine M. Steele link to paper: 10.1371/journal.pone.0193106 Icons made by catkuro from www.

High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets

Publishing date: 2018-02-12 Published on: PLOS ONE summary: High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here, Ptior Madanecki et al present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program.

MEA Viewer: A high-performance interactive application for visualizing electrophysiological data

Publishing date: 2018-02-09 Published on: PLOS ONE summary: None authors: Daniel C. Bridges, Kenneth R. Tovar, Bian Wu, Paul K. Hansma, Kenneth S. Kosik link to paper: 10.1371/journal.pone.0192477 Icons made by catkuro from www.

Laser additive manufacturing of 3D meshes for optical applications

Publishing date: 2018-02-07 Published on: PLOS ONE summary: None authors: Khamis Essa, Aydin Sabouri, Haider Butt, Fawzia Hamed Basuny, Mootaz Ghazy, Mahmoud Ahmed El-Sayed link to paper: 10.1371/journal.pone.0192389 Icons made by catkuro from www.

Predicting outcome of Morris water maze test in vascular dementia mouse model with deep learning

Publishing date: 2018-02-07 Published on: PLOS ONE summary: None authors: Akinori Higaki, Masaki Mogi, Jun Iwanami, Li-Juan Min, Hui-Yu Bai, Bao-Shuai Shan, Masayoshi Kukida, Harumi Kan-no, Shuntaro Ikeda, Jitsuo Higaki, Masatsugu Horiuchi

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations

Publishing date: 2018-02-07 Published on: PLOS ONE summary: None authors: Bhakti Dwivedi, Jeanne Kowalski link to paper: 10.1371/journal.pone.0192563 Icons made by catkuro from www.flaticon.com

Loop Assembly: a simple and open system for recursive fabrication of DNA circuits

Publishing date: 2018-01-18 Published on: bioRxiv summary: High efficiency methods for DNA assembly are based on sequence overlap between fragments or Type IIS restriction endonuclease cleavage and ligation. These have enabled routine assembly of synthetic DNAs of increased size and complexity.

Improving mapping for Ebola response through mobilising a local community with self-owned smartphones: Tonkolili District, Sierra Leone, January 2015

Publishing date: 2018-01-03 Published on: PLOS ONE summary: During the 2014–16 Ebola virus disease (EVD) outbreak, the Magburaka Ebola Management Centre (EMC) operated by Médecins Sans Frontières (MSF) in Tonkolili District, Sierra Leone, identified that available district maps lacked up-to-date village information to facilitate timely implementation of EVD control strategies.

Choose an open source license

Publishing date: 2018-01-01 Published on: Choose a license summary: A tool from GitHub helping developers choose an open source license for their source code. authors: GitHun, Inc. link to paper: https://choosealicense.

General design procedure for free and open-source hardware for scientific equipment

Publishing date: 2017-12-30 Published on: Designs summary: An open source toolkit for science is useful, but an open source toolkit that follows formal design principles might be even more so - improving interoperability, reproducibility and quality of designs.

A microfluidic thermometer: Precise temperature measurements in microliter- and nanoliter-scale volumes

Publishing date: 2017-12-28 Published on: PLOS ONE summary: These authors took up the challenge of creating a thermometer for accurate measurements of biological and chemical samples on the microliter or nanoliter scale.

Accelerating science and improving equitable access to hands-on STEM education through open science hardware | Gathering for Open Science Hardware

Publishing date: 2017-12-05 Published on: GOSH News summary: The US National Science Foundation (NSF) recently published a call for suggestions of research areas that could benefit from ‘networks of networks’ between US and international researchers.

openmta | BioBricks Foundation

Publishing date: 2017-12-01 Published on: BioBricks Foundation summary: The Open Material Transfer Agreement (OpenMTA) is a simple, standardized legal tool that enables individuals and organizations to share their materials on an open basis.

Sample treatment platform for automated integration of microextraction techniques and liquid chromatography analysis

Publishing date: 2017-12-01 Published on: AfricaOSH summary: AfricaOSH is a gathering for everyone interested in Open Science & Hardware as a means to achieve locally adapted, culturally relevant, technologically and economically feasible production in Africa; as an alternative to traditional Intellectual Property (IP )and closed knowledge systems; and to understand its potential for development and collaboration across Africa, especially by reducing barriers to entry in education, research and manufacturing.

The quest for open science

Publishing date: 2017-11-25 Published on: TechRadar summary: On the face of it, Dr Bowman’s story is that he’s on a three-year project to build a general-purpose 3D-printed microscope, but his ambitions are bigger and, ultimately, he wants to create 3D-printable ‘building blocks’ that others can use to make affordable, new experimental apparatus.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

Publishing date: 2017-11-15 Published on: PLOS ONE summary: In this exciting design, the authors present a large-field of view fluorescence chamber for visualisation of, well, anything that fluoresceses. Using LEDs and low-cost acrylics the system is set-up to allow for convenient simultaneous imaging in multiple colours using an RGB camera.

Democratizing science with the aid of parametric design and additive manufacturing: Design and fabrication of a versatile and low-cost optical instrument for scattering measurement

Publishing date: 2017-11-07 Published on: PLOS ONE summary: This paper focuses on the application of rapid prototyping techniques using additive manufacturing in combination with parametric design to create low-cost, yet accurate and reliable instruments.

Episode 46: From side project to startup

Publishing date: 2017-10-31 Published on: Podtail summary: This episode Science: Disrupt chatted to Bethan Wolfenden, the co-founder of Bento Bioworks, a biotech startup that has created a ‘laptop size laboratory’. This kit allows the user to perform simple DNA analysis and dramatically reduces the cost of the components you’d need to analyse samples, thus lowering the barrier to entry for molecular biology.

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Publishing date: 2017-10-27 Published on: bioRxiv summary: Björn Grüning and colleagues here present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors.

Imagining the “open” university: Sharing scholarship to improve research and education

Publishing date: 2017-10-24 Published on: PLOS Biology summary: Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education as well as increase the impact universities can have beyond their own walls.

Ethoscopes: An open platform for high-throughput ethomics

Publishing date: 2017-10-19 Published on: PLOS Biology summary: This design is a rig for high-throughput behavioural experiments with genetically amenable model species such as fruit flies. At its core, it is a webcam (RPi camera) focussed at a set of interchangable behavioural arena arrays for parallel recording of multiple aninals at once.

Episode 44: Leading the automation revolution

Publishing date: 2017-10-10 Published on: Podtail summary: In this episode Science: Disrupt chatted to Kristin Ellis, the Scientific Development Lead at OpenTrons, about all things science. OpenTrons is a company that builds affordable open-source lab robots, that remove the need to perform tedious manual pipetting tasks, to free up valuable time for researchers.

A programmable optical stimulator for the Drosophila eye

Publishing date: 2017-10-01 Published on: HardwareX summary: A programmable optical stimulator for Drosophila eyes is presented. The target application of the stimulator is to induce retinal degeneration in fly photoreceptor cells by exposing them to light in a controlled manner.

Open-source automated external defibrillator

Publishing date: 2017-10-01 Published on: HardwareX summary: The Automated External Defibrillator (AED) is a medical device that analyzes a patient’s electrocardiogram in order to establish whether he/she is suffering from the fatal condition of Sudden Cardiac Arrest (SCA), and subsequently allows the release of a therapeutic dose of electrical energy (i.

MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites

Publishing date: 2017-09-25 Published on: PLOS ONE summary: This paper presents the MRI Quality Control tool (MRIQC), a tool for extracting quality measures and fitting a binary (accept/exclude) classifier. The results show that the tool performs with high accuracy in intra-site prediction, but performance on unseen sites leaves space for improvement

What is the “Source” of Open Source Hardware?

Publishing date: 2017-09-05 Published on: Journal of Open Hardware summary: Based on analysis of public documentation of 132 products, this paper provides an overview of how practitioners tend to interpret the concept of open source hardware.

Free and open-source automated 3-D microscope

Publishing date: 2017-08-01 Published on: Appropedia summary: This paper presents a low-cost, open-source microscope 3-D stage. A RepRap 3-D printer was converted to an optical microscope equipped with a customized, 3-D printed holder for a USB microscope.

Open-source mobile water quality testing platform

Publishing date: 2017-08-01 Published on: Appropedia summary: This project details an open source water testing platform derived from the open-source colorimeter, which is made from open source electronics and 3-D printable components.

Open-source Wax RepRap 3-D Printer for Rapid Prototyping Paper-Based Microfluidics

Publishing date: 2017-08-01 Published on: Appropedia summary: This study reports on the development of a RepRap upgrade capable of converting a Prusa Mendel RepRap into a wax 3-D printer for paper-based microfluidic applications.

A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter

Publishing date: 2017-07-26 Published on: PLOS ONE summary: An easy to build, affordable open source turbidostat built with 3D printed parts and an Arduino. Additionaly it uses an algorithm based on Kalman filter that can be easily adapted for different uses such as bioreactors, studies of evolution or metabolic changes.

Feasibility of a 3D-printed anthropomorphic patient-specific head phantom for patient-specific quality assurance of intensity-modulated radiotherapy

Publishing date: 2017-07-20 Published on: PLOS ONE summary: None authors: Ji Woon Yea, Jae Won Park, Sung Kyu Kim, Dong Youn Kim, Jae Gu Kim, Chan Young Seo, Won Hyo Jeong, Man Youl Jeong, Se An Oh

The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans

Publishing date: 2017-07-18 Published on: PLOS Biology summary: The paper describes a €100 portable and neurogenetics lab. Built with off the shelf components and 3D printed parts it is a versatile tool that due to its modular design can be useful in different fields.

The Language of Glove: Wireless gesture decoder with low-power and stretchable hybrid electronics

Publishing date: 2017-07-12 Published on: PLOS ONE summary: This interesting paper shows that with $100 it is possible to construct a glove that uses include the ability to detect and translate sign language as well as to control a prosthetic hand.

Smartphone schlieren and shadowgraph imaging

Publishing date: 2017-07-11 Published on: Optics and Lasers in Engineering summary: This paper demonstrates a number of different schlieren and shadowgraph setups and image examples based only on a smartphone, its software applications, and some inexpensive accessories.

A method for rapid 3D scanning and replication of large paleontological specimens

Publishing date: 2017-07-05 Published on: PLOS ONE summary: None authors: Anshuman J. Das, Denise C. Murmann, Kenneth Cohrn, Ramesh Raskar link to paper: 10.1371/journal.pone.0179264 Icons made by catkuro from www.flaticon.com

Scientometric and patentometric analyses to determine the knowledge landscape in innovative technologies: The case of 3D bioprinting

Publishing date: 2017-06-29 Published on: PLOS ONE summary: Knowledge clusters and expert drivers indicate that there is a research focus on tissue engineering including the fabrication of organs, bioinks and new 3D bioprinting systems.

A lab-on-phone instrument with varifocal microscope via a liquid-actuated aspheric lens (LAL)

Publishing date: 2017-06-26 Published on: PLOS ONE summary: None authors: Yiin-Kuen Fuh, Zheng-Hong Lai, Li-Han Kau, Hung-Jui Huang link to paper: 10.1371/journal.pone.0179389 Icons made by catkuro from www.flaticon.com

A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays

Publishing date: 2017-06-16 Published on: PLOS ONE summary: A pipetting robot built with off the shelf components and small number of custom parts, it not only makes tedious processes automated, but it can also be used for improvement of experimental designs.

Open-source, community-driven microfluidics with Metafluidics

Publishing date: 2017-06-07 Published on: Nature Biotechnology summary: Metafluidics, an open-source, community-driven repository that hosts digital design files, assembly specifications, and open-source software to enable users to build, configure, and operate a microfluidic device.

3D printing and milling a real-time PCR device for infectious disease diagnostics

Publishing date: 2017-06-06 Published on: PLOS ONE summary: The paper describes a DIY affordable real-time PCR system, that works with one eppendorf tube at a time. Intentionally designed this way, the system is optimised for infectious disease diagnostics, and to be simple to build and maintain.

F.Lab’s DIYbio Centrifuge

Publishing date: 2017-05-31 Published on: Thingiverse summary: This DIYbio 3D printed centrifuge is a safe and fun piece of lab equipment, if built and operated carefully . authors: F.Lab link to paper: http://www.

From medical imaging data to 3D printed anatomical models

Publishing date: 2017-05-31 Published on: PLOS ONE summary: To lower the barrier to entry and provide the best options when aiming to 3D print an anatomical model from medical images, the authors provide an overview of relevant free and open-source image segmentation tools as well as 3D printing technologies.

Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes

Publishing date: 2017-05-19 Published on: Scientific Reports summary: The ability to reliably and precisely deliver picolitre volumes is an important component of biological research. The authors describe a high-performance, low-cost, open hardware pressure ejection system (Openspritzer), which can be constructed from off the shelf components.

An open source, wireless capable miniature microscope system

Publishing date: 2017-05-17 Published on: Journal of Neural Engineering summary: This paper describes a miniature microscope for single-photon fluorescence imaging in freely behaving animals made from 3D printed parts and off-the-shelf components.

Fabrication of malleable three-dimensional-printed customized bolus using three-dimensional scanner

Publishing date: 2017-05-11 Published on: PLOS ONE summary: A three-dimensional (3D)-printed customized bolus (3D bolus) can be used for radiotherapy application to irregular surfaces. However, bolus fabrication based on computed tomography (CT) scans is complicated and also delivers unwanted irradiation.

Characterization of 3D printing techniques: Toward patient specific quality assurance spine-shaped phantom for stereotactic body radiation therapy

Publishing date: 2017-05-04 Published on: PLOS ONE summary: This study suggests that a 3D-printed phantom simulating a high-density (about 1.4 g/cm3) organ can be created based on CT images and that a developed 3D printed spine phantom could be utilized in patient-specific quality assurance for stereotactic body radiation therapy.

FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila

Publishing date: 2017-04-28 Published on: PLOS ONE summary: This paper describes a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving D.

InMAP: A model for air pollution interventions

Publishing date: 2017-04-19 Published on: PLOS ONE summary: InMAP (Intervention Model for Air Pollution) offers an alternative to comprehensive air quality models for estimating the air pollution health impacts of emission reductions and other potential interventions.

An open source pharma roadmap

Publishing date: 2017-04-18 Published on: PLOS Medicine summary: Editors note: This paper offers ideas and suggestion for new and open source ways of developing drugs and treatments. The idea is to rely on the open source philosophy and have companies/non-profits/academics/government working together in an open setting.

phylo-node: A molecular phylogenetic toolkit using Node.js

Publishing date: 2017-04-14 Published on: PLOS ONE summary: None authors: Damien M. O’Halloran link to paper: 10.1371/journal.pone.0175480 Icons made by catkuro from www.flaticon.com

Cost and time-effective method for multi-scale measures of rugosity, fractal dimension, and vector dispersion from coral reef 3D models

Publishing date: 2017-04-13 Published on: PLOS ONE summary: None authors: G. C. Young, S. Dey, A. D. Rogers, D. Exton link to paper: 10.1371/journal.pone.0175341 Icons made by catkuro from www.flaticon.com

Upon the Shoulders of Giants: Open-Source Hardware and Software in Analytical Chemistry

Publishing date: 2017-04-05 Published on: Analytical Chemistry summary: The authors write to introduce analytical chemists who are new to the open-source movement to best practices and concepts in this area and to survey the state of open-source research in analytical chemistry.

Low-cost feedback-controlled syringe pressure pumps for microfluidics applications

Publishing date: 2017-04-03 Published on: PLOS ONE summary: Editors note: This paper describes how to build a closed loop control system for microfluidics, based on Arduino and 3D printed parts. It improves on existing syringe pumps as this system has a feedback loop that measures the pressure in the system and allows for more precise control of the volumes injected.

Gathering for Open Science Hardware 2017: building a movement

Publishing date: 2017-03-27 Published on: PLOS Blogs summary: Read about the GOSH 2017 and catch up on some of the highlights from Santiago, Chile. authors: Andre Maia Chagas, Max Liboiron, Jenny Molloy, Juan Manuel Garcia Arcos and Jeffrey Warren

An efficient and cost effective FPGA based implementation of the Viola-Jones face detection algorithm

Publishing date: 2017-03-25 Published on: HardwareX summary: None authors: Peter Irgens, Curtis Bader, Theresa Lé, Devansh Saxena, Cristinel Ababei link to paper: http://doi.org/10.1016/j.ohx.2017.03.002 Icons made by catkuro from www.flaticon.com

VorteX Clustering Environment

Publishing date: 2017-03-23 Published on: Github summary: VorteX is a graphical tool for cluster analysis of multiparametric datasets in biology, especially single-cell data. It provides multithreaded implementations of clustering algorithms, including nonparametric density-based X-shift, Hierarchical clustering, Mean-shift and K-medoids.

Gathering for Open Science Hardware 2017

Publishing date: 2017-03-22 Published on: GOSH summary: The Gathering for Open Science Hardware (GOSH) is a diverse, global community working to enhance the sharing of open, scientific technologies. In 2017 GOSH goal is to build a roadmap to bring together the people, skills and tools needed to make open science hardware ubiquitous by 2025

GOSH Community Forum

Publishing date: 2017-03-22 Published on: GOSH summary: This is the right place for discussions about the 2017 Gathering for Open Science Hardware that takes place in Santiago, Chile. Read notes on sessions here.

Emerging Business Models for Open Source Hardware

Publishing date: 2017-03-21 Published on: Journal of Open Hardware summary: The rise of Free and Open Source models for software development has catalyzed the growth of Free and Open Source hardware (also known as “Libre Hardware”).

NicoLase—An open-source diode laser combiner, fiber launch, and sequencing controller for fluorescence microscopy

Publishing date: 2017-03-16 Published on: PLOS ONE summary: None authors: Philip R. Nicovich, James Walsh, Till Böcking, Katharina Gaus link to paper: 10.1371/journal.pone.0173879 Icons made by catkuro from www.flaticon.com

CuboCube: Student creation of a cancer genetics e-textbook using open-access software for social learning

Publishing date: 2017-03-07 Published on: PLOS Biology summary: CuboCube is an open-source learning materials creation system designed to facilitate e-textbook development, with an ultimate goal of improving the social learning experience for students.

Interactive reconstructions of cranial 3D implants under MeVisLab as an alternative to commercial planning software

Publishing date: 2017-03-06 Published on: PLOS ONE summary: The use of implants that are specificaly designed for each patient is currently bounded to the use of expensive software or by the use of open source alternatives that are time consuming and labour intensive.

Microsco-pi: a novel and inexpensive way of merging biology and IT

Publishing date: 2017-03-06 Published on: Sussex Research Online summary: None authors: Jonathan P Bacon, Harry R Kent link to paper: http://sro.sussex.ac.uk/66499/ Icons made by catkuro from www.flaticon.com

CuboCube = Learn Better with Free Social Knowledgebase

Publishing date: 2017-03-04 Published on: cubocube summary: CuboCube is an open-source learning materials creation system designed to facilitate e-textbook development, with an ultimate goal of improving the social learning experience for students.

Mindboggling morphometry of human brains

Publishing date: 2017-02-23 Published on: PLOS Computational Biology summary: None authors: Arno Klein, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

Publishing date: 2017-02-21 Published on: PLOS Computational Biology summary: Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa.

Open Design 3D-Printable Adjustable Micropipette that meets ISO Standard for Accuracy

Publishing date: 2017-02-20 Published on: bioRxiv summary: None authors: Martin Brennan, Fahad Bokhari, David Eddington link to paper: http://biorxiv.org/content/early/2017/02/20/109231 Icons made by catkuro from www.flaticon.com

A time-sorting pitfall trap and temperature datalogger for the sampling of surface-active arthropods

Publishing date: 2017-02-16 Published on: HardwareX summary: Editors note: This paper describes a nifty and high-throughput way to collect bugs in the field while continuously monitoring the temperature as well as the time when each animal fell into each trap.

Interactive reconstructions of cranial 3D implants under MeVisLab as an alternative to commercial planning software - Cranial Defect Datasets

Publishing date: 2017-02-16 Published on: figshare summary: Interactive reconstructions of cranial 3D implants under MeVisLab as an alternative to commercial planning software. See https://doi.org/10.1371/journal.pone.0172694 for more details. authors: Egger et al

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour

Publishing date: 2017-02-03 Published on: PLOS Computational Biology summary: None authors: Stephanie Evans, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C. Coles, Marika C. Kullberg, Jon Timmis, Kieran Alden link to paper: 10.

Collective behavior quantification on human odor effects against female Aedes aegypti mosquitoes—Open source development

Publishing date: 2017-02-02 Published on: PLOS ONE summary: The method proposed contributes towards (a) unlimited open source use, (b) a low-cost setup, (c) complete guide for any entomologist to adapt in terms of hardware and software, (d) simple to use, and (e) a lightweight data output for collective behavior analysis of mosquitoes.

Individualized 3D printing navigation template for pedicle screw fixation in upper cervical spine

Publishing date: 2017-02-02 Published on: PLOS ONE summary: Pedicle screw fixation in the upper cervical spine is a difficult and high-risk procedure. The screw is difficult to place rapidly and accurately, and can lead to serious injury of spinal cord or vertebral artery.

Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC)

Publishing date: 2017-02-02 Published on: PLOS ONE summary: A new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. The system consists of a commercial brightfield microscope with one hardware modification—an inexpensive 3D printed condenser insert.

Open-Source Automated Mapping Four-Point Probe

Publishing date: 2017-01-26 Published on: Materials summary: Scientists have begun using self-replicating rapid prototyper (RepRap) 3-D printers to manufacture open source digital designs of scientific equipment. This approach is refined here to develop a novel instrument capable of performing automated large-area four-point probe measurements.

Vigi4Med Scraper: A Framework for Web Forum Structured Data Extraction and Semantic Representation

Publishing date: 2017-01-25 Published on: PLOS ONE summary: None authors: Bissan Audeh, Michel Beigbeder, Antoine Zimmermann, Philippe Jaillon, Cédric Bousquet link to paper: 10.1371/journal.pone.0169658 Icons made by catkuro from www.flaticon.com

Application of 3D printing to prototype and develop novel plant tissue culture systems

Publishing date: 2017-01-19 Published on: Plant Methods summary: None authors: Mukund R. Shukla, Amritpal S. Singh, Kevin Piunno, Praveen K. Saxena, A. Maxwell P. Jones link to paper: https://plantmethods.biomedcentral.com/articles/10.1186/s13007-017-0156-8 Icons made by catkuro from www.

A 3D Printed Toolbox for Opto-Mechanical Components

Publishing date: 2017-01-18 Published on: PLOS ONE summary: Editors note: The article presents a toolbox for opto-mechanical pieces that are based on printable 3D models and commercially available parts; each piece is tested for stability and precision and compared to pieces from well-known manufacturers.

WiseEye: Next Generation Expandable and Programmable Camera Trap Platform for Wildlife Research

Publishing date: 2017-01-11 Published on: PLOS ONE summary: The development of a user-customisable open source camera trap platform named ‘WiseEye’, designed to provide flexible camera trap technology for wildlife researchers.

Chaos-Based Simultaneous Compression and Encryption for Hadoop

Publishing date: 2017-01-10 Published on: PLOS ONE summary: None authors: Muhammad Usama, Nordin Zakaria link to paper: 10.1371/journal.pone.0168207 Icons made by catkuro from www.flaticon.com

A Modular and Affordable Time-Lapse Imaging and Incubation System Based on 3D-Printed Parts, a Smartphone, and Off-The-Shelf Electronics

Publishing date: 2016-12-21 Published on: PLOS ONE summary: The ATLIS enables the transformation of simple inverted microscopes into live cell imaging systems using custom-designed 3D-printed parts, a smartphone, and off-the-shelf electronic components.

Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes

Publishing date: 2016-12-13 Published on: bioRxiv summary: None authors: Chris J Forman, Hayley Tomes, Buchule Mbobo, Tom Baden, Joseph V Raimondo link to paper: http://biorxiv.org/content/early/2016/12/13/093633 Icons made by catkuro from www.

DropletKitchen Projects

Publishing date: 2016-12-05 Published on: DropletKitchen summary: None authors: DropletKitchen link to paper: https://dropletkitchen.github.io/pages/projects.html Icons made by catkuro from www.flaticon.com

Peek Hardware – Vision and Health for Everyone

Publishing date: 2016-12-05 Published on: Peek summary: None authors: Peek link to paper: http://www.peekvision.org/peek-hardware/#retina Icons made by catkuro from www.flaticon.com

An Assemblable, Multi-Angle Fluorescence and Ellipsometric Microscope

Publishing date: 2016-12-01 Published on: PLOS ONE summary: A multi-functional microscope for research laboratories that have significant cost and space limitations. The microscope pivots around the sample, operating in upright, inverted, side-on and oblique geometries.

Open Source Laboratory Sample Rotator Mixer and Shaker

Publishing date: 2016-10-14 Published on: HardwareX summary: None authors: Karankumar C. Dhankania, Joshua M. Pearce link to paper: http://www.sciencedirect.com/science/article/pii/S2468067216300049 Icons made by catkuro from www.flaticon.com

LudusScope: Accessible Interactive Smartphone Microscopy for Life-Science Education

Publishing date: 2016-10-05 Published on: PLOS ONE summary: An accessible, interactive do-it-yourself smartphone microscopy platform that promotes exploratory stimulation and observation of microscopic organisms, in a design that combines the educational modalities of build, play, and inquire.

A DIY Ultrasonic Signal Generator for Sound Experiments

Publishing date: 2016-10-04 Published on: arXiv summary: None authors: Ihab F. Riad link to paper: https://arxiv.org/abs/1610.00492 Icons made by catkuro from www.flaticon.com

An open source automatic feeder for animal experiments

Publishing date: 2016-09-06 Published on: HardwareX summary: This paper describes an open source experimental feeder using an Arduino microcontroller. The design of the feeder is focused on simplicity to provide a straight-forward building process and allow custom modifications for various requirements.

A fast multispectral light synthesiser based on LEDs and a diffraction grating

Publishing date: 2016-08-25 Published on: Scientific Reports summary: None authors: Gregor Belušič, Marko Ilić, Andrej Meglič and Primož Pirih link to paper: http://www.nature.com/articles/srep32012 Icons made by catkuro from www.flaticon.com

3D Printed Multimaterial Microfluidic Valve

Publishing date: 2016-08-15 Published on: PLOS ONE summary: 3D printing multi-property programmable fluidic devices in a single step, in which integrated multimaterial valves can be used to control complex fluidic reactions for a variety of applications, including DNA assembly and analysis, continuous sampling and sensing, and soft robotics

3D-Printing for Analytical Ultracentrifugation

Publishing date: 2016-08-15 Published on: PLOS ONE summary: None authors: Abhiksha Desai, Jonathan Krynitsky, Thomas J. Pohida, Huaying Zhao, Peter Schuck link to paper: 10.1371/journal.pone.0155201 Icons made by catkuro from www.

Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as a Tool in Cell Biology Education

Publishing date: 2016-08-15 Published on: PLOS ONE summary: A strategy to increase the engagement of students into the world of cell and structural biology by combining 3D electron microscopy techniques and 3D prototyping technology (3D printing) to generate 3D physical models that accurately and realistically reproduce a close-to-the native structure of the cell and serve as a tool for students and teachers outside the main centers.

Gathering for Open Science Hardware - GOSH Manifesto

Publishing date: 2016-07-25 Published on: Gathering for Open Science Hardware summary: None authors: Gathering for Open Science Hardware link to paper: http://openhardware.science/gosh-manifesto/ Icons made by catkuro from www.flaticon.com

Open-source Hardware Statement of Principles and Definition

Publishing date: 2016-07-25 Published on: Open Source Hardware Association summary: None authors: Open Source Hardware Association link to paper: http://www.oshwa.org/definition/ Icons made by catkuro from www.flaticon.com

MECs: Building Blocks for Creating Biological and Chemical Instruments

Publishing date: 2016-07-20 Published on: PLOS ONE summary: Each MEC “building block” performs a fundamental function that is commonly found in biological or chemical instruments, functions like valving, pumping, mixing, controlling, and sensing.

Meeting debrief and next steps: The Challenge of Attribution, or “View Source,” in 3D Printing

Publishing date: 2016-07-15 Published on: Creative Commons summary: None authors: Jane Park link to paper: https://creativecommons.org/2016/07/15/meeting-debrief-next-steps-challenge-attribution-view-source-3d-printing/ Icons made by catkuro from www.flaticon.com

Magnetic stirrer from a 80 mm fan by WaveSupportApparatus - Thingiverse

Publishing date: 2016-07-08 Published on: Thingiverse summary: None authors: WaveSupportApparatus link to paper: http://www.thingiverse.com/thing:1663540 Icons made by catkuro from www.flaticon.com

A 3D Printed Toolbox for Opto-Mechanical Components - PDF DOWNLOAD

Publishing date: 2016-06-30 Published on: arXiv summary: None authors: Luis Jose Salazar-Serrano, Juan P. Torres, Alejandra Valencia link to paper: http://arxiv.org/pdf/1606.09563.pdf Icons made by catkuro from www.flaticon.com

Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

Publishing date: 2016-06-30 Published on: PLOS ONE summary: None authors: Kamfai Chan, Mauricio Coen, Justin Hardick, Charlotte A. Gaydos, Kah-Yat Wong, Clayton Smith, Scott A. Wilson, Siva Praneeth Vayugundla, Season Wong

Accessible bioprinting: adaptation of a low-cost 3D-printer for precise cell placement and stem cell differentiation

Publishing date: 2016-06-07 Published on: IOPscience summary: None authors: John A Reid, Peter A Mollica, Garett D Johnson, Roy C Ogle, Robert D Bruno and Patrick C Sachs link to paper: http://iopscience.

The Desktop Muon Detector: A simple, physics-motivated machine- and electronics-shop project for university students

Publishing date: 2016-06-03 Published on: arXiv summary: None authors: Spencer N. Axani, Janet M. Conrad, Conor Kirby link to paper: https://arxiv.org/abs/1606.01196 Icons made by catkuro from www.flaticon.com

Open source expansion cloud chamber

Publishing date: 2016-05-26 Published on: Hackaday.io summary: None authors: M. Bindhammer link to paper: https://hackaday.io/project/11896-open-source-expansion-cloud-chamber Icons made by catkuro from www.flaticon.com

Lasercut Optics Bench

Publishing date: 2016-04-13 Published on: Hackaday.io summary: None authors: Peter Walsh link to paper: https://hackaday.io/project/10707-lasercut-optics-bench Icons made by catkuro from www.flaticon.com

UCLA Miniscope

Publishing date: 2016-04-13 Published on: miniscope.org summary: None authors: Golshani Lab, Silva Lab, Khakh Lab link to paper: http://miniscope.org/index.php?title=Main_Page Icons made by catkuro from www.flaticon.com

3D printed microscopy imaging chambers

Publishing date: 2016-04-01 Published on: Github summary: None authors: Ben Goodnow, PRNicovich link to paper: https://github.com/PRNicovich/BenlideChambers Icons made by catkuro from www.flaticon.com

Arduino Due based tool to facilitate in vivo two-photon excitation microscopy

Publishing date: 2016-04-01 Published on: Biomed Opt Express summary: None authors: Pietro Artoni, Silvia Landi, Sebastian Sulis Sato, Stefano Luin, Gian Michele Ratto link to paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933559/ Icons made by catkuro from www.

$10 Smartphone to digital microscope conversion!

Publishing date: 2016-03-21 Published on: Instructables summary: None authors: Yoshinok link to paper: http://www.instructables.com/id/10-Smartphone-to-digital-microscope-conversion/ Icons made by catkuro from www.flaticon.com

Ball bearing dispenser

Publishing date: 2016-03-21 Published on: Docubricks summary: None authors: Neil Pearson link to paper: http://docubricks.com/projects/ball-bearing-dispenser-4mm-for-dna-extraction-library-prep Icons made by catkuro from www.flaticon.com

BrainMap: ECE 4760 Final Project

Publishing date: 2016-03-21 Published on: BrainMap summary: None authors: Patrick Dear, Mark Bunney, Jr. link to paper: http://people.ece.cornell.edu/land/courses/ece4760/FinalProjects/s2012/pmd68_mab448/pmd68_mab448/index.html Icons made by catkuro from www.flaticon.com

Build a Gel Electrophoresis Chamber (PDF download)

Publishing date: 2016-03-21 Published on: Genetic Science Learning Centre summary: None authors: Louisa A. Stark, Lisa Romero de Mendoza, Rob Wheeler link to paper: http://teach.genetics.utah.edu/content/labs/build_gel_box.pdf Icons made by catkuro from www.

Cheap DIY GFP (Green Fluorescent Protein) Illuminator

Publishing date: 2016-03-21 Published on: Make summary: None authors: Eri Gentry link to paper: http://makezine.com/2011/03/04/cheap-diy-gfp-green-fluorescent-protein-illuminator/ Icons made by catkuro from www.flaticon.com

DIY microscopy

Publishing date: 2016-03-21 Published on: Hackteria summary: None authors: MArc Dusseiller link to paper: http://hackteria.org/wiki/DIY_microscopy Icons made by catkuro from www.flaticon.com

DIY Oil Pollution Testing

Publishing date: 2016-03-21 Published on: Instructables summary: None authors: PublicLab link to paper: http://www.instructables.com/id/DIY-Oil-Pollution-Testing/ Icons made by catkuro from www.flaticon.com

Gel electrophoresis system (mini)

Publishing date: 2016-03-21 Published on: Instructables summary: None authors: jorodeo link to paper: http://www.instructables.com/id/Gel-electrophoresis-system-mini/ Icons made by catkuro from www.flaticon.com

Home-Built STM

Publishing date: 2016-03-21 Published on: Dan Berard summary: None authors: Dan Berard link to paper: http://dberard.com/home-built-stm/ Icons made by catkuro from www.flaticon.com

How to build a $21 gel box

Publishing date: 2016-03-21 Published on: Citizen Science Quarterly summary: None authors: Citizen Science Quarterly link to paper: http://citizensciencequarterly.com/2011/10/cheapass-science-gel-box/ Icons made by catkuro from www.flaticon.com

Lego Microtome

Publishing date: 2016-03-21 Published on: Instructables summary: None authors: Lemonie link to paper: http://www.instructables.com/id/Lego-Microtome/?ALLSTEPS Icons made by catkuro from www.flaticon.com

Make a Gel Electrophoresis Power Supply

Publishing date: 2016-03-21 Published on: Make summary: None authors: John Baichtal link to paper: http://makezine.com/2013/10/19/make-a-gel-electrophoresis-power-supply/ Icons made by catkuro from www.flaticon.com

Old microscope + £100 (+ 3D printer) = GFP fluorescent microscope

Publishing date: 2016-03-21 Published on: David Molnar summary: None authors: David Molnar link to paper: http://dm516.user.srcf.net/?p=107 Icons made by catkuro from www.flaticon.com

OpenAFM | Developing low-cost open-source science tools for schools.

Publishing date: 2016-03-21 Published on: OpenAFM summary: None authors: OpenAFM link to paper: http://openafm.com/ Icons made by catkuro from www.flaticon.com

Parametric Gel Electrophoresis System

Publishing date: 2016-03-21 Published on: Docubricks summary: None authors: Tobias Wenzel link to paper: http://docubricks.com/projects/parametric-gel-electrophoresis-system Icons made by catkuro from www.flaticon.com

Public Lab: Desktop Spectrometry Kit 3.0

Publishing date: 2016-03-21 Published on: Public Lab summary: None authors: Warren link to paper: https://publiclab.org/wiki/desktop-spectrometry-kit-3-0 Icons made by catkuro from www.flaticon.com

ramanPi - Raman Spectrometer • Hackaday.io

Publishing date: 2016-03-21 Published on: Hackaday.io summary: None authors: fl@c@ link to paper: https://hackaday.io/project/1279-ramanpi-raman-spectrometer Icons made by catkuro from www.flaticon.com

Stromlinet Nano - Nanoscience Made Easy

Publishing date: 2016-03-21 Published on: Stromlinet Nano summary: None authors: Stromlinet Nano link to paper: http://www.stromlinet-nano.com/ Icons made by catkuro from www.flaticon.com

A tiny and accurate pH-meter: from schematic to calibration

Publishing date: 2016-03-17 Published on: Damien Douxchamps summary: None authors: Damien Douxchamps link to paper: http://damien.douxchamps.net/elec/ph_meter/ Icons made by catkuro from www.flaticon.com

Open Hardware pH meter

Publishing date: 2016-03-17 Published on: GitHub summary: None authors: hephesto/phduino link to paper: https://github.com/hephesto/phduino Icons made by catkuro from www.flaticon.com

Open-source lab jack

Publishing date: 2016-03-17 Published on: Thingiverse summary: None authors: jpearce link to paper: http://www.thingiverse.com/thing:28298 Icons made by catkuro from www.flaticon.com

OS-Vortex-Mixer: 3D printed vortex mixer (needs motor, bearing, micro switch, tripple throw switch, power supply)

Publishing date: 2016-03-17 Published on: GitHub summary: None authors: jdkizer link to paper: https://github.com/jdkizer/OS-Vortex-Mixer Icons made by catkuro from www.flaticon.com

Platform Jack [Fully Assembled, No Supports]

Publishing date: 2016-03-17 Published on: Thingiverse summary: None authors: Intentional3D link to paper: http://www.thingiverse.com/thing:925556 Icons made by catkuro from www.flaticon.com

NightLife: A cheap, robust, LED based light trap for collecting aquatic insects in remote areas

Publishing date: 2016-03-14 Published on: Biodiversity Data Journal summary: None authors: Benjamin Price, Ed Baker link to paper: http://bdj.pensoft.net/articles.php?id=7648&instance_id=2236763 Icons made by catkuro from www.flaticon.com

3D-Printing for Analytical Ultracentrifugation

Publishing date: 2016-02-23 Published on: arxiv.org summary: None authors: Abhiksha Desai, Jonathan Krynitsky, Thomas J. Pohida, Huaying Zhao, Peter Schuck link to paper: http://arxiv.org/abs/1602.07181# Icons made by catkuro from www.flaticon.com

A one-piece 3D printed microscope and flexure translation stage

Publishing date: 2016-02-15 Published on: arXiv.org summary: None authors: James P. Sharkey, Darryl C. W. Foo, Alexandre Kabla, Jeremy J. Baumberg, Richard W. Bowman link to paper: http://arxiv.org/abs/1509.05394 Icons made by catkuro from www.

BabyLegs

Publishing date: 2016-02-15 Published on: Civic Laboratory summary: None authors: Max Liboiron link to paper: http://civiclaboratory.nl/2015/05/31/babylegs/ Icons made by catkuro from www.flaticon.com

C12666MA Micro-Spectrometer

Publishing date: 2016-02-15 Published on: Hackaday.io summary: None authors: Pure Engineering link to paper: https://hackaday.io/project/4141-c12666ma-micro-spectrometer Icons made by catkuro from www.flaticon.com

DOLPi - RasPi Polarization Camera

Publishing date: 2016-02-15 Published on: Hackaday.io summary: None authors: David Prutchi link to paper: https://hackaday.io/project/6958-dolpi-raspi-polarization-camera Icons made by catkuro from www.flaticon.com

PCB agitator from an old CD ROM

Publishing date: 2016-02-15 Published on: Instructables.com summary: None authors: mzsolt link to paper: http://www.instructables.com/id/PCB-agitator-from-an-old-CR-ROM/ Icons made by catkuro from www.flaticon.com

Photosynq

Publishing date: 2016-02-15 Published on: GitHub summary: None authors: PhotosynQ Project - Michigan State University’s Plant Research Lab link to paper: https://github.com/Photosynq Icons made by catkuro from www.flaticon.com

Plastic Eating Device for Rocky Ocean Coasts

Publishing date: 2016-02-15 Published on: Civic Laboratory summary: None authors: Cian Kavanagh, Colin Grenning, Nicolas Brouard-Ayres link to paper: http://civiclaboratory.nl/2015/05/31/p-e-d-r-o-ck/ Icons made by catkuro from www.flaticon.com

A one-piece 3D printed flexure translation stage for open-source microscopy

Publishing date: 2016-02-08 Published on: AIP Scientific Instruments summary: None authors: James P. Sharkey, Darryl C. W. Foo, Alexandre Kabla, Jeremy J. Baumberg and Richard W. Bowman link to paper: http://scitation.

Open-Source Selective Laser Sintering (OpenSLS) of Nylon and Biocompatible Polycaprolactone

Publishing date: 2016-02-03 Published on: PLOS ONE summary: None authors: Ian S. Kinstlinger, Andreas Bastian, Samantha J. Paulsen, Daniel H. Hwang, Anderson H. Ta, David R. Yalacki, Tim Schmidt, Jordan S.

BluBEAM - a scanning laser microscope

Publishing date: 2016-01-15 Published on: Hackaday.io summary: None authors: Andreas Betz link to paper: https://hackaday.io/project/9205-blubeam-a-scanning-laser-microscope Icons made by catkuro from www.flaticon.com

LIFE3D CAPSULE

Publishing date: 2016-01-13 Published on: Wevolver summary: None authors: Tristan Schoony link to paper: https://www.wevolver.com/wevolver.staff/life3d-capsule/main/description/ Icons made by catkuro from www.flaticon.com

OPENROV V2.8 MINI OBSERVATION CLASS ROV

Publishing date: 2016-01-13 Published on: Wevolver summary: None authors: OpenROV Community link to paper: https://www.wevolver.com/openrov.community/openrov/main/description/ Icons made by catkuro from www.flaticon.com

Ultrascope Explorer

Publishing date: 2016-01-13 Published on: Wevolver summary: None authors: OSA Projects link to paper: https://www.wevolver.com/osa.projects/ultrascope/hardware/description/ Icons made by catkuro from www.flaticon.com

Quartz Crystal Microbalance: the first scientific QCM entirely Open Source

Publishing date: 2016-01-06 Published on: openQCM summary: None authors: Raffaele Battaglia, Gianluca Ferrini, Marco Mauro, Glenda Torres Guizado link to paper: http://openqcm.com/ Icons made by catkuro from www.flaticon.com

A Simple DIY Stereoscopic Microscope

Publishing date: 2016-01-01 Published on: funsci summary: None authors: G. Carboni link to paper: http://www.funsci.com/fun3_en/uster2/uster2.htm Icons made by catkuro from www.flaticon.com

PrusaHand

Publishing date: 2016-01-01 Published on: PrusHand summary: None authors: Jan Horky link to paper: http://prusahand.org/ Icons made by catkuro from www.flaticon.com

DNA Assembly in 3D Printed Fluidics

Publishing date: 2015-12-30 Published on: PLOS ONE summary: None authors: William G. Patrick, Alec A. K. Nielsen, Steven J. Keating, Taylor J. Levy, Che-Wei Wang, Jaime J. Rivera, Octavio Mondragón-Palomino, Peter A.

BioHack Academy

Publishing date: 2015-12-03 Published on: GitHub summary: None authors: BioHack Academy link to paper: https://github.com/biohackacademy Icons made by catkuro from www.flaticon.com

Low cost and open source bio-engineering kit

Publishing date: 2015-12-03 Published on: Hackaday.io summary: None authors: M. Bindhammer link to paper: https://hackaday.io/project/8205-low-cost-and-open-source-bio-engineering-kit Icons made by catkuro from www.flaticon.com

Medical tricorder

Publishing date: 2015-12-03 Published on: Hackaday.io summary: None authors: M. Bindhammer link to paper: https://hackaday.io/project/4693-medical-tricorder Icons made by catkuro from www.flaticon.com

Open LED Illuminator: A Simple and Inexpensive LED Illuminator for Fast Multicolor Particle Tracking in Neurons

Publishing date: 2015-11-23 Published on: PLOS ONE summary: None authors: Jens B. Bosse, Nikhila S. Tanneti, Ian B. Hogue, Lynn W. Enquist link to paper: 10.1371/journal.pone.0143547 Icons made by catkuro from www.

OpenPCR

Publishing date: 2015-10-27 Published on: OpenPCR summary: None authors: OpenPCR link to paper: http://openpcr.org/ Icons made by catkuro from www.flaticon.com

OpenSPIM Wiki

Publishing date: 2015-10-27 Published on: OpenSPIM summary: None authors: OpenSPIM link to paper: http://openspim.org/Welcome_to_the_OpenSPIM_Wiki Icons made by catkuro from www.flaticon.com

Open Source Physics

Publishing date: 2015-10-21 Published on: Compadre summary: None authors: Open Source Physics link to paper: http://www.compadre.org/osp/ Icons made by catkuro from www.flaticon.com

Open Source Toolkit: Hardware

Publishing date: 2015-10-21 Published on: PLOS Collections Blog summary: None authors: Andre Maia Chagas, Tom Baden link to paper: http://blogs.plos.org/collections/open-source-toolkit-hardware/ Icons made by catkuro from www.flaticon.com

Generic Lab Equipement

Publishing date: 2015-10-06 Published on: GaudiLab summary: None authors: GaudiLab link to paper: http://www.gaudi.ch/GaudiLabs/?page_id=328 Icons made by catkuro from www.flaticon.com

Hackaday.io

Publishing date: 2015-10-06 Published on: Hackaday.io summary: None authors: Hackaday link to paper: https://hackaday.io Icons made by catkuro from www.flaticon.com

Hackteria

Publishing date: 2015-10-06 Published on: Hackteria summary: None authors: Hackteria link to paper: http://hackteria.org/wiki/Main_Page Icons made by catkuro from www.flaticon.com

low-field MRI

Publishing date: 2015-10-06 Published on: Hackaday.io summary: None authors: Peter Jansen link to paper: https://hackaday.io/project/5030-low-field-mri Icons made by catkuro from www.flaticon.com

NeuroBytes

Publishing date: 2015-10-06 Published on: Hackaday.io summary: None authors: zakqwy link to paper: https://hackaday.io/project/3339-neurons-neurons-neurons Icons made by catkuro from www.flaticon.com

Open Ephys

Publishing date: 2015-10-06 Published on: Open Ephys summary: None authors: Open Ephys link to paper: http://www.open-ephys.org/ Icons made by catkuro from www.flaticon.com

Open Hardware Repository

Publishing date: 2015-10-06 Published on: CERN summary: None authors: CERN link to paper: http://www.ohwr.org/ Icons made by catkuro from www.flaticon.com

Open Syringe Pump

Publishing date: 2015-10-06 Published on: Hackaday.io summary: None authors: naroom, triplefunny link to paper: https://hackaday.io/project/1838-open-syringe-pump Icons made by catkuro from www.flaticon.com

open-stent

Publishing date: 2015-10-06 Published on: cbonsig summary: None authors: cbonsig link to paper: https://github.com/cbonsig/open-stent Icons made by catkuro from www.flaticon.com

OpenBionics | An open-source initiative for low-cost, light-weight, underactuated robot hands and prosthetic devices.

Publishing date: 2015-10-06 Published on: OpenBionics summary: None authors: Minas Liarokapis, Agisilaos Zisimatos, Christoforos Mavrogiannis, George Kontoudis link to paper: http://www.openbionics.org/ Icons made by catkuro from www.flaticon.com

Opensource Arduino Spectrometer

Publishing date: 2015-10-06 Published on: mySpectral summary: None authors: Andrej Mosat, Filip Stefunko, Michal Kostic, Vincent Touquet link to paper: http://myspectral.com/#download Icons made by catkuro from www.flaticon.com

OS CT Scanner

Publishing date: 2015-10-06 Published on: Tricorder project summary: None authors: Peter Jansen link to paper: http://www.tricorderproject.org/blog/tag/openct/ Icons made by catkuro from www.flaticon.com

TakkTile

Publishing date: 2015-10-06 Published on: TakkTile summary: None authors: Leif Jentoft, Yaroslav Tenzer et al link to paper: http://www.takktile.com/ Icons made by catkuro from www.flaticon.com

The Open Hand Project

Publishing date: 2015-10-06 Published on: Open Hand Project summary: None authors: Joel Gibbard link to paper: http://www.openhandproject.org/ Icons made by catkuro from www.flaticon.com

Open Data Formats for Cosmic Rays

Publishing date: 2015-08-19 Published on: Cosmic Pi summary: None authors: Hugo Day link to paper: http://cosmicpi.org/?p=14 Icons made by catkuro from www.flaticon.com

Open-Source Photometric System for Enzymatic Nitrate Quantification

Publishing date: 2015-08-05 Published on: PLOS ONE summary: The development of an inexpensive portable, handheld photometer will greatly expedite field nitrate analysis to combat pollution. To accomplish this goal, a methodology for the design, development, and technical validation of an improved open-source water testing platform capable of performing Nitrate Reductase Nitrate-Nitrogen Analysis Method is evaluated.

Multi-Contrast Imaging and Digital Refocusing on a Mobile Microscope with a Domed LED Array

Publishing date: 2015-05-13 Published on: PLOS ONE summary: None authors: Zachary F. Phillips, Michael V. D’Ambrosio, Lei Tian, Jared J. Rulison, Hurshal S. Patel, Nitin Sadras, Aditya V. Gande, Neil A.

The Accuracy of a Method for Printing Three-Dimensional Spinal Models

Publishing date: 2015-04-27 Published on: PLOS ONE summary: None authors: Ai-Min Wu, Zhen-Xuan Shao, Jian-Shun Wang, Xin-Dong Yang, Wan-Qing Weng, Xiang-Yang Wang, Hua-Zi Xu, Zhong-Ke Lin, Yong-Long Chi link to paper: 10.

Strengthening of 3D Printed Fused Deposition Manufactured Parts Using the Fill Compositing Technique

Publishing date: 2015-04-16 Published on: PLOS ONE summary: None authors: Joseph T. Belter, Aaron M. Dollar link to paper: 10.1371/journal.pone.0122915 Icons made by catkuro from www.flaticon.com

Fabricating optical lenses by inkjet printing and heat-assisted in situ curing of polydimethylsiloxane for smartphone microscopy

Publishing date: 2015-03-30 Published on: SPIE | Journal of Biomedical Optics summary: None authors: Yu-Lung Sung, Jenn Jeang, Chia-Hsiung Lee, Wei-Chuan Shih link to paper: http://biomedicaloptics.spiedigitallibrary.org/article.aspx?articleid=2279353 Icons made by catkuro from www.

A Biotic Game Design Project for Integrated Life Science and Engineering Education

Publishing date: 2015-03-25 Published on: PLOS Biology summary: None authors: Nate J. Cira, Alice M. Chung, Aleksandra K. Denisin, Stefano Rensi, Gabriel N. Sanchez, Stephen R. Quake, Ingmar H. Riedel-Kruse

Open Labware: 3-D Printing Your Own Lab Equipment

Publishing date: 2015-03-20 Published on: PLOS Biology summary: None authors: Tom Baden, Andre Maia Chagas, Greg Gage, Timothy Marzullo, Lucia L. Prieto-Godino, Thomas Euler link to paper: 10.1371/journal.pbio.1002086 Icons made by catkuro from www.

The Aerodynamic Cost of Head Morphology in Bats: Maybe Not as Bad as It Seems

Publishing date: 2015-03-04 Published on: PLOS ONE summary: None authors: Dieter Vanderelst, Herbert Peremans, Norizham Abdul Razak, Edouard Verstraelen, Greg Dimitriadis link to paper: 10.1371/journal.pone.0118545 Icons made by catkuro from www.

colorimeter

Publishing date: 2015-03-03 Published on: mtu-most summary: None authors: mtu-most link to paper: https://github.com/mtu-most/colorimeter Icons made by catkuro from www.flaticon.com

DIY CO2 Incubator Bioreactor for Mammalian Cell Culture

Publishing date: 2014-12-14 Published on: Pelling Lab summary: None authors: Pelling Lab link to paper: https://www.pellinglab.net/single-post/diy/DIY-CO2-Incubator-Bioreactor-for-Mammalian-Cell-Culture Icons made by catkuro from www.flaticon.com

A low-cost programmable pulse generator for physiology and behavior | Frontiers in Neuroengineering

Publishing date: 2014-12-11 Published on: Frontiers in Neuroengineering summary: None authors: Joshua I. Sanders and Adam Kepecs link to paper: http://journal.frontiersin.org/article/10.3389/fneng.2014.00043/full Icons made by catkuro from www.flaticon.com

The Design and Construction of an Electrohydrodynamic Cartesian Robot for the Preparation of Tissue Engineering Constructs

Publishing date: 2014-11-18 Published on: PLOS ONE summary: None authors: Shaikh Hafeez Hashimdeen, Mark Miodownik, Mohan J. Edirisinghe link to paper: 10.1371/journal.pone.0112166 Icons made by catkuro from www.flaticon.com

A Customized Bolus Produced Using a 3-Dimensional Printer for Radiotherapy

Publishing date: 2014-10-22 Published on: PLOS ONE summary: None authors: Shin-Wook Kim, Hun-Joo Shin, Chul Seung Kay, Seok Hyun Son link to paper: 10.1371/journal.pone.0110746 Icons made by catkuro from www.flaticon.com

A High Performance, Cost-Effective, Open-Source Microscope for Scanning Two-Photon Microscopy that Is Modular and Readily Adaptable

Publishing date: 2014-10-21 Published on: PLOS ONE summary: None authors: David G. Rosenegger, Cam Ha T. Tran, Jeffery LeDue, Ning Zhou, Grant R. Gordon link to paper: 10.1371/journal.pone.0110475 Icons made by catkuro from www.

The OpenPicoAmp: An Open-Source Planar Lipid Bilayer Amplifier for Hands-On Learning of Neuroscience

Publishing date: 2014-09-24 Published on: PLOS ONE summary: None authors: Vadim Shlyonsky, Freddy Dupuis, David Gall link to paper: 10.1371/journal.pone.0108097 Icons made by catkuro from www.flaticon.com

Open-Source Syringe Pump Library

Publishing date: 2014-09-17 Published on: PLOS ONE summary: None authors: Bas Wijnen, Emily J. Hunt, Gerald C. Anzalone, Joshua M. Pearce link to paper: 10.1371/journal.pone.0107216 Icons made by catkuro from www.

The Billion Cell Construct: Will Three-Dimensional Printing Get Us There?

Publishing date: 2014-06-17 Published on: PLOS Biology summary: None authors: Jordan S. Miller link to paper: 10.1371/journal.pbio.1001882 Icons made by catkuro from www.flaticon.com

Is Your System Calibrated? MRI Gradient System Calibration for Pre-Clinical, High-Resolution Imaging

Publishing date: 2014-05-07 Published on: PLOS ONE summary: None authors: James O’Callaghan, Jack Wells, Simon Richardson, Holly Holmes, Yichao Yu, Simon Walker-Samuel, Bernard Siow, Mark F. Lythgoe link to paper: 10.

An Open Source 3-D Printed Modular Micro-Drive System for Acute Neurophysiology

Publishing date: 2014-04-15 Published on: PLOS ONE summary: None authors: Shaun R. Patel, Kaushik Ghose, Emad N. Eskandar link to paper: 10.1371/journal.pone.0094262 Icons made by catkuro from www.flaticon.com

Openstage: A Low-Cost Motorized Microscope Stage with Sub-Micron Positioning Accuracy

Publishing date: 2014-02-26 Published on: PLOS ONE summary: None authors: Robert A. A. Campbell, Robert W. Eifert, Glenn C. Turner link to paper: 10.1371/journal.pone.0088977 Icons made by catkuro from www.flaticon.com

RIVETS: A Mechanical System for In Vivo and In Vitro Electrophysiology and Imaging

Publishing date: 2014-02-14 Published on: PLOS ONE summary: None authors: Jason E. Osborne, Joshua T. Dudman link to paper: 10.1371/journal.pone.0089007 Icons made by catkuro from www.flaticon.com

Talon Hand

Publishing date: 2014-01-19 Published on: Thingiverse summary: None authors: Peter Binkley, Peregrine Hawthorn, Ivan Owen, Richard Van As, Michael Curry link to paper: http://www.thingiverse.com/thing:229620 Icons made by catkuro from www.flaticon.com

At last, a DIY programable water bath

Publishing date: 2013-12-08 Published on: LabFab.cc summary: None authors: ZAMANLUI link to paper: http://blog.labfab.cc/?p=47 Icons made by catkuro from www.flaticon.com

3D-Printed Microwell Arrays for Ciona Microinjection and Timelapse Imaging

Publishing date: 2013-12-06 Published on: PLOS ONE summary: None authors: Clint Gregory, Michael Veeman link to paper: 10.1371/journal.pone.0082307 Icons made by catkuro from www.flaticon.com

The Open Access Malaria Box: A Drug Discovery Catalyst for Neglected Diseases

Publishing date: 2013-06-17 Published on: PLOS ONE summary: None authors: Thomas Spangenberg, Jeremy N. Burrows, Paul Kowalczyk, Simon McDonald, Timothy N. C. Wells, Paul Willis link to paper: 10.1371/journal.pone.0062906 Icons made by catkuro from www.

Open-Source Colorimeter

Publishing date: 2013-04-19 Published on: Sensors summary: This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter.

Open-Source 3D-Printable Optics Equipment

Publishing date: 2013-03-27 Published on: PLOS ONE summary: None authors: Chenlong Zhang, Nicholas C. Anzalone, Rodrigo P. Faria, Joshua M. Pearce link to paper: 10.1371/journal.pone.0059840 Icons made by catkuro from www.

Closed-Loop, Multichannel Experimentation Using the Open-Source NeuroRighter Electrophysiology Platform | Frontiers in Neural Circuits

Publishing date: 2013-01-18 Published on: Frontiers in Neural Circuits summary: None authors: Jonathan P. Newman, Riley Zeller-Townson, Ming-Fai Fong, Sharanya Arcot Desai, Robert E. Gross, and Steve M. Potter link to paper: http://journal.

A Simple, Low-Cost Conductive Composite Material for 3D Printing of Electronic Sensors

Publishing date: 2012-11-21 Published on: PLOS ONE summary: None authors: Simon J. Leigh, Robert J. Bradley, Christopher P. Purssell, Duncan R. Billson, David A. Hutchins link to paper: 10.1371/journal.pone.0049365 Icons made by catkuro from www.

Portable Liquid Chromatography - PDF download

Publishing date: 2012-10-01 Published on: RSC summary: None authors: Akihiko Ishida, Takehiro Fujimoto, Satoshi Yokogawa, Hirofumi Tani, Manabu Tokeshi, Ichiro Yanagisawa link to paper: http://www.rsc.org/images/loc/2012/pdf/T.4.111.pdf Icons made by catkuro from www.

The SpikerBox: A Low Cost, Open-Source BioAmplifier for Increasing Public Participation in Neuroscience Inquiry

Publishing date: 2012-03-21 Published on: PLOS ONE summary: None authors: Timothy C. Marzullo, Gregory J. Gage link to paper: 10.1371/journal.pone.0030837 Icons made by catkuro from www.flaticon.com

Improving robot manipulation through fingertip perception

Publishing date: 2012-01-10 Published on: Intelligent Autonomous Systems summary: None authors: Alexis Maldonado, Humberto Alvarez Heredia, and Michael Beetz link to paper: https://ias.in.tum.de/ Icons made by catkuro from www.flaticon.com

CheapStat: An Open-Source, “Do-It-Yourself” Potentiostat for Analytical and Educational Applications

Publishing date: 2011-09-13 Published on: PLOS ONE summary: None authors: Aaron A. Rowe, Andrew J. Bonham, Ryan J. White, Michael P. Zimmer, Ramsin J. Yadgar, Tony M. Hobza, Jim W. Honea, Ilan Ben-Yaacov, Kevin W.

Portable, Battery-Operated, Low-Cost, Bright Field and Fluorescence Microscope

Publishing date: 2010-08-04 Published on: PLOS ONE summary: None authors: Andrew R. Miller, Gregory L. Davis, Z. Maria Oden, Mohamad Reza Razavi, Abolfazl Fateh, Morteza Ghazanfari, Farid Abdolrahimi, Shahin Poorazar, Fatemeh Sakhaie, Randall J.

About

We are network of collaborators trying to keep track and curate interesting open source projects that have been published as peer reviewed or preprints. If you have a project that you’d like to see listed here or if you know of a project that should be listed, drop us a line, via E-mail, or Twitter.

Team

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André Maia Chagas

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Jenny Molloy

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Tom Baden

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