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Infography: a bioinformatics tools overview

The field of bioinformatics is constantly evolving at a rapid pace. Grasping its latest developments and trends can be challenging for tool developers that wish to create accurate and up-to-date solutions that match life scientists’ needs.   Be aware of the current status of the field can be of importance for a variety of reason. For example, knowing the most popular programming language in bioinformatics can give you an advantage when applying for a position, and identifying the top tool-funding agencies can help you get the grant you need to develop your tool. For this, we created a dashboard of interactive figures to provide an overview of the field of bioinformatics tool development, accompanied with a series of blogposts to …

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DataOnTools #6: OMICtools features

With more than 29,000 entities, OMICtools is the largest collection of bioinformatics tools. Our classification system allows to easily find and identify the tools you need. We conclude our series by providing some data analysis on the OMICtools collection. Tool categorization system In OMICtools software and database are classified in one main category among transcriptomics, genomics, phenomics, metabolomics, proteomics and epigenomics. Then, they are labelled in one or more of the 2,000 subcategories. To explore OMICtools categories, check our interactive figure (Figure 1, available online).   Obsolescence in bioinformatics tools Tools are developed continuously, and usually hosted on institution servers and corporate websites. Eventually, their URLs will not be maintained and the tool will become inaccessible, obsolete.   OMICtools scans …

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Getting Started with the Pipeline Generator

As a biologist, you probably know that the key to good data analysis is the selection and use of appropriate software. Owing to the increasing complexity of biological data, the number of tools typically required to perform an analysis is constantly growing, rendering the selection of software even more difficult. Indeed, finding the best series of tools that match your analysis criteria is challenging.   A pipeline is a series of software presented in a logical order. With your data as a starting point, a pipeline shows you the right pathway of tools to perform your analysis.   Until now, finding the optimal workflow was very challenging because pipelines are difficult to decipher or remain buried in the masses of biomedical texts. To …

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DataOnTools #4: Evolution of tool specifications

When it comes to developing a bioinformatics software tool, many different languages can be used. Moreover, developers might have to choose on which operating systems among the most used they want their creation to be run. Finally, the target audience of the software (personal use, free distribution or commercial distribution) may influence the usage of the software (web interface, desktop, etc.).   Users can run bioinformatics software tools either on the web, locally on a desktop or server, or both. While tools that can be used on the web could be expected to be more common, reflecting the need for user-friendliness for less-skilled users, we in fact found that more than 69% of the 20,918 tools registered as software are …

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DataOnTools #1: A comprehensive data analysis of bioinformatics tools

Ever wondered how many tools are released each year? What country or institute produce the most tool? Or what are the most used programming languages? To answer these burning questions, and a lot more, we are launching a new series of articles, DataOnTools, providing a wide range of data on bioinformatics tools evolution and current status. Most of these data representation will be freely accessible and reusable.   DataOnTools, everything you always wanted to know about bioinformatics tools   Just like the data they are built to analyze, bioinformatics tools are growing at an exponential pace. The origin of bioinformatics tools is well documented and can be traced back to the late 60s. However, documenting the evolution of tools in …

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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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