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Clément Levin

How to use omicX search engine like a pro

In the past few months, we’ve brought amazing new features on omicX, getting closer to our dream of democratizing bioinformatics to scientists.   To ensure you did not miss anything and make your experience 100% efficient, we are launching a new series of tutorials that cover the full functionality of omicX. Scientist spend a lot of time searching for the right bioinformatics tools. There are so many tools, but also so many languages to write (or use) them that finding the good one is a difficult task. Along with the most comprehensive catalog of bioinformatics resources, we have developed a powerful and intelligent search engine for retrieving what you need in one-click.   Let’s review all the things you can …

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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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Best bioinformatics software for mass-cytometry analysis

Conventional flow cytometry is limited by the number of fluorochromes and cell markers that can be targeted at once. Overcoming this limitation, mass-cytometry combines mass-spectrometry and flow cytometry by using metal-conjugated antibodies to label cellular proteins and extend the number of markers to be targeted.   A combination of spectrometry and cytometry   In mass-cytometry, antibodies are conjugated with isotopically pure elements, and these antibodies are used to label cellular proteins. Cells are nebulized and sent through an argonplasma, which ionizes the metal-conjugated antibodies. The metal signals are then analyzed by a time-of-flight mass spectrometer. The approach overcomes limitations of spectral overlap in flow cytometry by utilizing discrete isotopes as a reporter system instead of traditional fluorophores which have broad emission spectra.   Due to its numerous advantages (minimal …

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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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DataOnTools #5: Tools in the literature

Scientific communications and publications are the best way to promote your work – whether you are a tool developer or a bioinformatician conducting analysis. In this article, we analyze tools publications to explore a new aspect of the evolution of the field of bioinformatics. Tool publications and citation In the OMICtools database, nearly eight out of ten have been published in a peer-reviewed journal, with 41.7% of all tools cited at least once, while 36.0% have never been cited in the literature (Figure 1a). Among those with a PMID, about half of them have never been cited in the literature, and the other half has been cited at least once. This is of importance because citations are the best way …

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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 #3: Economics of tool development

Like any other research field, bioinformatics and software development are highly depend on funding. By extracting grants and other funding sources from tool publication, we provide a new insight on the economics of tool development.   Funding is a critical aspect of tool development. We ranked the sources of funding agencies associated with a total of 12,761 published tools to assess the top 20 tool-funding agencies worldwide (Figure 1). Nearly half of all published tools were funded by the National Institutes of Health (NIH) or the National Science Foundation (NSF), both US-based agencies.     Countries’ themselves take a critical role in funding research through national grants. Indeed figure 2 shows a high correlation (r=0.81; p<0.0001) between a country’s research …

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DataOnTools #2: Tool development and collaboration worldwide

Bioinformatics tools are developed by research laboratories, university, and private companies that often publish their work in scientific journals. In fact, nearly 80% of all tools registered on OMICtools have a PMID, and thus are accompanied with a scientific publication. By tracking authors affiliations, we provide a unique perspective on worldwide tool development and collaboration between countries.   Tool development worldwide   Tool development and publication is dominated by the USA, with 30% of published tools originating from US institutions (Figure 1a and b).     Most leading tool-developing institutions are hosted by European and American continents, with 18 out of the top 20 tool-developing institutes and universities located in the USA, United Kingdom, Canada, or rest of Europe (Figure …

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