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Identifying the right bioinformatics tools for biological data

In the biology big data context, managing the amount and diversity of data that experiments produce is a challenging task. Depending on the scope of your research, you probably spend a lot of your time searching for the right bioinformatics tools.   Like most, you probably have a general idea of how to analyze your data and have used more than one tool. If you’re working in a computational biology laboratory, you’ve probably heard the question “What is the best software for genome sequence alignment?” or “What algorithm is the standard for sequence alignment in genetics?” While BLAST is probably the most popular tool for this, there are lots of other tools for mining, and aligning biological data.  So choosing the right solution for …

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Document your research with electronic lab notebooks

Laboratory notebook are an essential component of the scientific research process. They are used to document hypotheses, experiments and results, and can also serve a role in protecting intellectual property, among many other functions. However, their use is limited when a large number of researchers are working on a same project, and pasting digital results in the era of big data can be challenging. Electronic lab notebook to the rescue Electronic lab notebooks (ELNs) were first adopted by the pharmaceutical industry, and are now progressively (but slowly) entering the academic research area. Now several open-source and commercial solutions are proposed to researchers. There main advantages include long-term storage, optimization of data reproducibility, support for collaboration and sharing, and the ability …

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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, …

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OMICtools uses code versioning to enhance tool traceability

Software tools on the Web evolve over time, with developers adding or removing features to improve their product, making code versioning an essential aspect of sustainable software development. Reliable code versioning allows developers to automatically track their work and revert to previous versions when needed.   Discover here how OMICtools can help you facilitate the traceability of your tool – and learn how to successfully upload your work in a community-controlled repository. Benefits of version control Provides a mechanism to keep track of code changes Allows you to track the history of changes, work on the same code files, and merge code from different branches Shows conflicts on code merges, allowing you to resolve them quickly Following the FAIR data principles The FAIR …

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3 tips to boost your OMICtools profile page

After four years on the road (OMICtools was launched in 2013), it was time to make some changes to our user profile – and a new front-end version has now been implemented! You can customize your profile page quickly and easily, with each section of the profile page re-worked and re-designed to streamline what you want the community to know about you.  Now’s the time to increase your visibility, and we can help you to succeed At OMICtools we strive to offer you a better way to identify the right tools for your biomedical data. Today, we are working to make OMICtools the number #1 biomedical community platform, which also allows you to network with your peers, and speed up your …

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Community members: your publication on arXiv.org!

Community experts, we’re pleased to inform you that you’re co-authors of the article titled OMICtools: a community-driven search engine for biological data analysis. The preprint version of this article has been assigned the permanent arXiv identifier 1707.03659 and is available on arXiv.org. This publication gives us the opportunity to thank all the OMICtools biocurators and users for their helpful collaboration in providing high-quality and updated information on bioinformatics tools. Overview of the collaborative functionality offers on the OMICtools platform Here’s the abstract: with high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational biology, in order to maximize the potential of their data. OMICtools is …

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Community opinion: optimize your search experience

Firstly, a big thanks to all of you who participated in our survey! A few weeks ago, we sent out a survey so we can better meet your needs and improve your search experience on OMICtools. Thanks to all of the 78 participants who took part in this survey, your feedback is really important to us. We are happy to report here the positive results of this survey. All of you were satisfied regarding the relevance of the results you get with the OMICtools search engine, with 59% judging the results as good and 31% as great. Participants also reported that for 55% of you find the OMICtools search engine and website easy to use and innovative, and 43% consider …

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How to make a software more robust

Scientific quality and reproducibility rely on the traceability of the experimental data, statistical methods and bioinformatics tools used to generate results. Being unable to replicate and validate scientific results is unfortunately very common. This reproducibility crisis as named by Monya Baker considerably slows down the research progress and affects all of the fields including chemistry, biology and medicine.   Best practices are crucially needed today to improve reproducibility of data analysis and hence to make software robust enough to be run by any user.   Indeed, most of the software tools used to produce scientific results and publications are prototypes and lack robustness. Usually designed and run by a single person in a specific computing environment, codes may be very …

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