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Credit your work and enter to win a pass for a congress

You designed a tool or performed specific tasks in software development? Spread the word! Credit your expertise with badges and enter to win a pass for a congress (and others exciting prizes). To participate, all you need to do is badge your contribution on the bioinformatics tools we reference.  Don’t hang around, the contest ends the 11th May. How does the contest work? Sign in to your account (or sign up for free if you aren’t already a member). Find the tools you designed (or contributed to design): use the search engine and filters to rapidly locate your project Click on the “set my contributions” button  to add badges Why are badges important? Badges are the best way to earn …

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Explore gene-expression datasets with the Omics Dashboard

The advent of omics technologies has fostered the generation of a flood of complex, high-resolution datasets, the analysis of which remains a major hurdle and requires conversion into actionable biological knowledge. To address this challenge, Peter Karp and his colleagues from the SRI Bioinformatics Research Group have developed the Omics Dashboard within the BioCyc.org website. Here, they present their tool and its main features. The Omics Dashboard The Dashboard provides a multi-level visual read out of an expression dataset, from the cellular level to the gene level.  The user can probe their data in a fast and intuitive manner to gain a deep understanding of the data at multiple biological levels.   At the highest echelon (Figure 1) the Dashboard provides …

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Best bioinformatics software for MS-based proteomics analysis

Proteomics are the next step after genomics and transcriptomics to study biological systems. However, analyzing the proteome is much more difficult than the genome or transcriptome, because each cell expresses its own set of proteins. Mass spectrometry (MS) has emerged as the most important and popular tool to identify, characterize, and quantify proteins and their post-translational modifications with high throughput and on a large scale (Zhang et al.). To help you perform your experiments in the best conditions, we asked the OMICtools community to choose the best MS-based untargeted proteomics analysis tools. LC-MS based untargeted proteomics Two-dimension liquid-chromatography (LC) coupled with mass-spectrometry (LC-MS) is the leading technology for high-throughput proteomics. LC is used to separate proteins from different samples in parallel, and …

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Finding scientific resources with semantic search engines

  The exponential growth of the number of biological studies over the past decade has created an enormous challenge to make effective use of the accumulated information. Owing to this size, simple web-style text search engines are often not yielding the best results and a lot of important information remains buried in the masses of text (Doms, 2005). Semantic technologies have been introduced for better question answering and faster literature exploration (Doms, 2008). They use ontologies to give an overview over large query results and guide scientists for discoveries. Starting your research in biology but don’t know which platform to use to find impactful studies? Here is a list of useful resources you will love using to retrieve articles and …

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Search and find olive oil compounds with OliveNet

Olive oil is now widely recognized as a key component of the health benefits provided by the “Mediterranean diet”. However, the exact composition and biological activity of olive oil and its compounds are still being investigated. OliveNet aims at gathering all information on olive oil compounds in a knowledgebase. Here, they briefly present their database and its features.   The benefits of olive oil   The health benefits of a Mediterranean diet rich in extra-virgin olive oil was illustrated by the classical Ancel Keys Seven Countries Study and more recently the methodical, multicentre Prevention with Mediterranean (PREDIMED), trial in Spain. In the context of health benefits the initial focus was on the major mono- and poly-unsaturated fatty acids, and accumulated …

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Decipher sequencing data with file formats for NGS

Next-generation sequencing (NGS) technologies generate tremendous amount of data. A typical human genome consists of ~3 billion base pairs to be sequenced. A critical step in NGS is to extract the information, stock it and transmit it in an easy-to-use and lightweight way. Why need file format? Coded in bits, a human genome would “only” weight about 700 MB (Reid Robison). However, sequencers generate short reads that redundantly span the sequence and then need to be aligned to a reference genome. Moreover, since sequencing is not perfect, every base has a score attached to it to evaluate the quality of sequencing. Thus, file formats have been developed to code a maximum of this information in a minimum of space. Here …

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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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How to run proteomics analysis with mass-spectrometry

Proteins are an essential component of living organisms. In the systems biology era, the large-scale analysis of proteins and proteomes has a lot of applications, such as identification and quantification of proteins, study of post-translational modifications, protein structure, protein-protein or protein-nucleic acid interactions.   Here, we will focus on mass-spectrometry, the leading technology for high-throughput proteomics, and how it is used for protein characterization.  High-throughput proteomics Solving the complexity of gene expression at the whole-organism level with genomics and transcriptomics was thought to be the key to understanding the processes of life. However, protein expression does not always correlate with gene expression because mRNA is not always translated into protein, because a single transcript can code for several proteins, and …

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