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What is protein function prediction?

Identifying the function of a previously unknown protein is a difficult task. While some technologies such as RNA interference enable to assess the function of a protein experimentally, they are often labor-intensive and cannot match the rate at which new sequences and genes are being identified with high-throughput sequencing techniques.   Prediction by computational methods has thus become a privileged way of identifying new functions of unknown proteins. Here, we will briefly present the most recent methods and resources in computational protein function prediction.   Protein functions   Protein function is a wide term that includes several aspects of a protein activity. Having a common vocabulary to describe protein functions is essential for function prediction and annotation. The Gene Ontology (GO) …

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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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How to use omicX protocols like a pro

We previously discussed all the cool things you can do with the omicX search engine. Here, we’ll uncover our latest and most exciting feature, omicX protocols, so you can analyze your big biodata like a pro. What it a computational protocol   We know that the number of publications in biology is skyrocketing, and it’s becoming more and more difficult for scientists to identify the latest trends, analysis methods and tools in their field.   Searching through publications to benchmark or identify the best combination of tools for your analysis can take hours. For this reason, we developed a new feature that automatically extracts and recreates protocols (logical series of bioinformatics tools designed to perform an analysis task) from free …

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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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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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