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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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Review a tool and enter to win an exciting prize

Checking the reviews section has become an integral component of the software selection process. When they are used strategically, positive reviews can really help identify the most accurate solutions.  As a community-driven platform, we need your input to review the must-have tools. Rules are simple: Post a review for a tool and enter to win a tablet. Don’t hang around, the contest ends the 5th of October. Why is your review important? Software review is an helpful process to assist developers in validating the quality of a project. It is also a great input for scientists that want to make informed decisions. Reviews offer a double advantage. As a user, you can rapidly identify which tools perform the best based on your peers’ experience. …

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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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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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