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How to use omicX statistics like a pro

omicX just launched statistics for tools, a new feature for software developers and users to get a bunch of knowledge about bioinformatics resources.   Let’s see how this will help you become a bigbio data pro!   Why it’s useful   While a few tools are being developed to address very specific needs, most of them aim at helping researchers for mainstream applications in genomics, transcriptomics, or proteomics. This leads to a lot of redundancy, and poses a problem for scientists: How to choose among several seemingly identical solutions?   The usual way of dealing with this problem is a painful, time-consuming review of the specs and literature, to optimize compatibility with other tools, or simply find the solution your …

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DataOnTools #6: omicX features

With more than 29,000 entities, omicX 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 omicX collection. Tool categorization system   Software tools 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 the 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.   omicX scans tools …

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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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