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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. 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 differentially-expressed genes are identified using statistical …

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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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Un(e) développeur(se) web – Expérimenté(e)

omicX est une société innovante et dynamique dans le domaine de la bioinformatique. Elle est à l’origine du projet OMICtools, une plateforme conçue pour aider les chercheurs et les cliniciens du monde entier à identifier les meilleurs outils d’analyse de données biologiques. Nous recherchons activement un(e) développeur(se) web pour rejoindre notre équipe et développer la plateforme. En plein essor, nous avons besoin d’un(e) collaborateur(rice) autonome, maîtrisant les standards actuels en développement web et ayant envie de s’investir dans une startup jeune et dynamique. Description du poste Amélioration et maintenance du site existant Modélisation de base de données Mise en place de plateformes de développement : wiki, espace clients et utilisateurs, pages de profils, système de publication de contenu, API Rest …

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Un(e) juriste spécialisé(e) en contrats et propriété intellectuelle

omicX est une société innovante et dynamique dans le domaine de la bioinformatique. Elle est à l’origine du projet OMICtools, une plateforme conçue pour aider les chercheurs et les cliniciens du monde entier à identifier les meilleurs outils d’analyse de données biologiques. En plein essor, nous recherchons un(e) collaborateur(rice) autonome et expérimenté(e) afin de renforcer la gestion administrative de la société. La mission sera d’assurer conseil et expertise juridique auprès de la direction, afin d’encadrer les aspects de propriété intellectuelle, de valorisation et de collaboration. Nous avons besoin d’un(e) collaborateur(rice) motivé(e) et polyvalent(e) ayant envie de s’investir dans une start-up en pleine expansion. Description du poste Rédiger, analyser, négocier, et veiller à la bonne exécution, en français et en anglais, …

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Un(e) ingénieur(e) en sécurité informatique

omicX est une société innovante et dynamique dans le domaine de la bioinformatique. Elle est à l’origine du projet OMICtools, une plateforme conçue pour aider les chercheurs et les cliniciens du monde entier à identifier les meilleurs outils d’analyse de données biologiques. Dans le cadre de son développement, omicX recherche un(e) collaborateur(rice) afin d’apporter une expertise sécurité à la société. Votre mission consiste à faire progresser le niveau de sécurité de l’entreprise en aidant les collaborateurs à mieux comprendre les risques et à connaître les bonnes pratiques. Vous interviendrez également en amont pour aider, conseiller et améliorer les projets de R&D et définir la stratégie de sécurité de l’entreprise. Descriptif du poste Vous assurerez  le bon fonctionnement de l’infrastructure technique …

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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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