Share your best tips with protocol repositories

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Research protocols are like good old recipes, they contain time-tested knowledge, and their secrets are not shared with anybody. However, due to the complexity of today’s experiments, it has become more important than ever for scientists to find and use the best protocols available. New “omics” technologies require precise and controlled sample preparation, and the smallest variation can lead to huge differences in the resulting output.

The need for protocol repositories

The “big data” has fostered the development of a number of repositories, for bioinformatics tools (OMICtools), software codes (GitHub), and peer-reviewed journals dedicated to protocols (Nature Protocols, JOVE).

Following this trend, a number of initiative propose to store and reference research protocols on so-called protocol repositories. These repositories share common features: they follow a collaborative and community model, and they are open-access. Here are some protocol repositories that might help you find the best protocol for your experiments.

Protocols.io:

Protocols.io is an online repository for scientific protocols that can be used at any point in the research cycle, before publication to be shared and run easily and in total confidentiality and/or during the manuscript submission process, as an alternative to the online Material & Methods section. Protocols.io is runnable as an iOS and Android application, and as already partnered with the journals Genetics and GigaScience to share protocols via the service instead of supplementary files.

To learn more, here is a video presentation of protocols.io: https://www.youtube.com/watch?time_continue=2&v=wvqw6PPl0eY

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Protocols.io gather a lot of protocols from users and can be run on smartphones.

Protocol Exchange:

The Protocol Exchange is an open resource from the journal Nature Protocols, where the community of scientists pool their experimental know-how. Users can discover new protocols, share a protocol, join a lab group, comment on protocols, and organize their favorite and personalize their experience.

Protocols added to protocol exchange are standardized and usually include the following section: Introduction, reagents and equipment, procedure and timing, troubleshooting, and anticipated results/figures.

The database contains protocols from any branch of science with a focus on protocols being used to answer outstanding biological and biomedical science research questions.

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Protocol Exchange homepage.

OpenWetWare (OWW):

OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. This website is a wiki that proposes to browse labs and groups around the world, to link to biology courses, protocols, and blogs to share all things related to biological sciences.

OWW also developed an online Lab Notebook where users can create dynamic calendars, create projects, etc.

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OpenWetWare homepage.

Of interest, other protocol repositories have been developed for specific research areas such as SDOP-DB for mouse phenotyping protocols or myExperiment for bioinformatics workflows.

So if you come up with a new protocol and you feel it could benefit the scientific community, don’t hesitate to use one of these useful repositories to make science go forward!

How documentation can improve your tools

Bioinformatics tools documentation and guidelines can come in handy when using a complicated piece of software. Yet, tools developers most often overlook the benefit of releasing documentation with their creations.

The main goal of tool documentation is to provide the basics of the software’s functionalities and guidelines on how to use it. Having such documentation will ensure great coverage and impact of your tool, as well as save you countless hours answering basic questions.

Different types of research software documentation

Software documentation can take various formats:

  • Manuscript, usually the original publication describing the tool.
  • Readme, which contains basic instructions for installation and use of the software.
  • Quickstart, a step-by-step protocol for installation and use of the software.
  • Reference manual, a comprehensive documentation of every configurable setting of the software.
  • FAQ, answers to most asked or anticipated questions.

Documentation-generating tools

Writing a comprehensive and easy-to-understand guideline can be a difficult task. For this, software have been developed to generate documentation directly from source codes. Here are some useful software that might help you create your documentation:

  • Doxygen: Generates documentation from source code. Supports most coding langages, including C++, C, Objective-C, C#, PHP, Java, Python, IDL and more. Doxygen can generate online documentation in HTML, or offline reference manuals in various formats. It can also extract code structure from undocumented source files.
  • Javadoc: Generates HTMP pages of application programming interfaces (APIs) documentation from Java source files.
  • Sphinx: Originally created for the Python documentation, this tool uses reStructuredText as its markup language and proposes various output formats (HTML, Latex, ePub, etc.), extensive cross-references, hierarchical structure, automatic indices, code handling, and more.
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Example of documentation generated with Sphinx.

To learn more on software documentation and general recommendations, read this useful paper by Karimzadeh and Hoffman: Top considerations for creating bioinformatics software documentation.

No excuses not to write documentation next time!

How playing games can help scientific research

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Ever felt that saving princess Zelda or “catching ‘em all” was not rewarding enough? If so, why don’t you help Science and play serious games?

In their wider definition, serious games are games designed for other purposes than pure entertainment. In scientific research, serious games have been developed to make the community of gamers participate in the resolution of complex problems that cannot be solved by machines.

Serious games in biomedical research

Indeed, humans are very efficient at recognising patterns, which is rather a difficult task for computers and algorithms. Serious games combine a pleasing interface, a challenging and entertaining problem to solve, and a will to help scientific research.  Problem to solve can be broke down into smaller tasks, which multiplied by the number of players can lead to great results.

How serious games can make a difference

A notable example of how serious games can make science go forward is the resolution of the crystal structure of the M-PMV virus retroviral protease. Stuck for more than 10 years on the resolution of its structure, researchers used the online protein-folding game “Foldit” and its community of gamers. After 3 weeks, the 3D structure of the protein was solved and published in Nature Structural & Molecular Biology.

Popular serious games also include “Phylo”, where players try to improve multiple sequence alignments by moving blocks, “EyeWire”, dedicated to 3D reconstruction of neurons, or “EteRNA”, where players design RNA sequences that fold into target secondary structures.

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Player interface from the serious games Phylo (up) and EyeWire (down).

Serious games are also used in human and public health, to raise awareness on specific diseases, or to help patients and their family deal with a medical condition. Their use is now spreading to a lot of different disciplines such as teaching, politics, ecology, etc.

If you want to contribute to research and science while having fun, check out these games:

  • MalariaSpot, to quantify malaria parasites on thick blood smears.
  • Dizeez, a multiple-choice quiz to catalog gene-disease associations.
  • The Cure, where you use your knowledge to make informed decisions about the best combinations of variables (e.g. genes) to build predictive patterns.
  • GenESP, a gene annotation game where players contribute their knowledge of gene function and disease relevance.

If you want to produce, publish, or promote your own game, visit Science Game Lab, a platform for the promotion of scientific games with a purpose.

Game on!

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