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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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Your top 3 RNA-seq read alignment tools

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 you to choose your favorite analysis tools step by step. Mapping reads to reference genome  After a first step of quality control (previous blog post here), 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 …

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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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Link splice-isoform expression to cancer metabolism with GEMsplice

Metabolic models rely on genes and proteins expression to estimate or predict a metabolic cell phenotype. In the case of cancer, it is now admitted that metabolism dysregulations play a crucial role in cancer onset and proliferation. However, most metabolic models only rely on gene expression, and do not account for splice-isoform expression and/or alteration.   To solve this gap, Claudio Angione developed GEMsplice, a desktop application that allows to link splice-isoform gene expression data to cancer metabolism. Here, he describes the features and benefits of GEMsplice. Solving the gap in cancer metabolism models Despite being often perceived as the main contributors to cell fate and physiology, genes alone cannot predict the cellular phenotype. A genome-scale analysis of cancer metabolism captures …

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