Clément Levin

Virtualize your computing with IaaS

Since the advent of high-throughput sequencing, the number and complexity of biological data has exploded. Though information technology and computers have paralleled this development, researchers rarely meet the computational power and storage capability required to perform the analysis of their data (Ben Langmead and Abhinav Nellore). Infrastructure as a service to the rescue For this, infrastructures as a service (IaaS) have been created to let users run large-scale computing workloads on the cloud – that is, on virtual machines hosted on dedicated infrastructures – and to stock up to exabits of data.   According to the National Institute of Standards and Technology, IaaS can be described as:   The capability provided to the consumer is to provision processing, storage, networks, …

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Track and control your code with version control systems

Software codes are constantly evolving, become more complex as newer versions are released. But sometimes errors and bugs occur and being able to retrieve the latest stable version of your software code can be a life-saver. For this, most software code repositories are equipped with version control systems (VCS). Why do you need version control and how is it implemented? Software developers working in teams are continually writing new source code and changing existing source code. The code for a project is typically organized in a folder structure or “file tree”. One developer on the team may be working on a new feature while another developer fixes an unrelated bug by changing code, each developer may make their changes in …

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Best bioinformatics software for RNA-seq quantification and differential expression

RNA-sequencing is progressively replacing microarrays for the study of transcriptomes, and comparison of gene expression. One advantage of this technique is the ability to identify and quantify the expression of isoforms and unknown transcripts. To help you perform your experiments in the best conditions, we are closing our series of surveys on RNA-sequencing by asking the OMICtools community to choose the best quantification and differential expression tools.   1. DESeq 2. Limma 3. EdgeR RNA quantification and differential expression While microarrays produce a numerical estimate of the relative expression of genes across the genome, RNA-sequencing experiments rely on read-count distributions. After mapping reads to a reference genome, the expression level for each gene or isoform are estimated and normalized, and finally …

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Document your research with electronic lab notebooks

Laboratory notebook are an essential component of the scientific research process. They are used to document hypotheses, experiments and results, and can also serve a role in protecting intellectual property, among many other functions. However, their use is limited when a large number of researchers are working on a same project, and pasting digital results in the era of big data can be challenging. Electronic lab notebook to the rescue Electronic lab notebooks (ELNs) were first adopted by the pharmaceutical industry, and are now progressively (but slowly) entering the academic research area. Now several open-source and commercial solutions are proposed to researchers. There main advantages include long-term storage, optimization of data reproducibility, support for collaboration and sharing, and the ability …

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Promoting standards in biological research

Most research advances are built upon pre-existing data and findings. This paradigm implies that researchers must be able to reproduce data on which they base their own research. Yet a number of promising pre-clinical researches do not go into clinics because of the inability to reproduce the work (Freedman and Inglese). For this, it has become essential to set standards and good practices in life sciences research. Initiatives promoting standards in biology A number of initiatives have been created to set and promote standards in biology research. Some society are proposing standards to cover all areas of basic research and clinics, while others are focusing on specific research fields. Here are some of the most advanced organizations which develop standards …

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Share your best tips with protocol repositories

Research protocols are like good old recipes, they contain time-tested knowledge, and their secrets are not shared with anybody. However, due to the complexity of today’s experiments, it has become more important than ever for scientists to find and use the best protocols available. New omics technologies require precise and controlled sample preparation, and the smallest variation can lead to huge differences in the resulting output. The need for protocol repositories The “big data” has fostered the development of a number of repositories, for bioinformatics tools (OMICtools), software codes (GitHub), and peer-reviewed journals dedicated to protocols (Nature Protocols, JOVE). Following this trend, a number of initiative propose to store and reference research protocols on so-called protocol repositories. These repositories share …

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Best bioinformatics software for RNA-seq read alignment

RNA-sequencing (RNA-seq) is currently the leading technology for transcriptome analysis. RNA-seq has a wide range of applications, from the study of alternative gene splicing, post-transcriptional modifications, to comparison of relative gene expression between different biological samples. To help you perform your RNA-seq experiments in the best conditions, we are continuing our series of surveys by asking the OMICtools community to choose the best analysis tools step by step.   Mapping reads to reference genome  After a first step of quality control, the next step in the analysis of your RNA-seq experiment is alignment of reads to a reference genome or a transcriptome database.   There are two types of aligners: Splice-unaware and splice-aware. Splice-unaware aligners are able to align continuous reads to a genome …

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How documentation can improve your tools

Bioinformatics tools documentation and guidelines can come in handy when using a complicated piece of software. Yet, tools developers most often overlook the benefit of releasing documentation with their creations.   The main goal of tool documentation is to provide the basics of the software’s functionalities and guidelines on how to use it. Having such documentation will ensure great coverage and impact of your tool, as well as save you countless hours answering basic questions. Different types of research software documentation Software documentation can take various formats: Manuscript, usually the original publication describing the tool Readme, which contains basic instructions for installation and use of the software Quickstart, a step-by-step protocol for installation and use of the software Reference manual, …

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