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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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How playing games can help scientific research

Ever felt that saving princess Zelda or “catching ‘em all” was not rewarding enough? If so, why don’t you help Science and play serious games? In their wider definition, serious games are games designed for other purposes than pure entertainment. In scientific research, serious games have been developed to make the community of gamers participate in the resolution of complex problems that cannot be solved by machines. Serious games in biomedical research Indeed, humans are very efficient at recognising patterns, which is rather a difficult task for computers and algorithms. Serious games combine a pleasing interface, a challenging and entertaining problem to solve, and a will to help scientific research.  Problem to solve can be broke down into smaller tasks, …

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Map functional networks of ncRNAs with circlncRNAnet

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) lack protein-coding potential but have nonetheless emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. These noncoding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. To fully capture, from a network perspective, the functional implications of lncRNAs or circRNAs of interest, Dr. Bertrand Chin-MingTan and his team have implemented an integrative bioinformatics approach to examine in silico the functional networks of non-coding RNAs. Here, they present their web server tool “circlncRNAnet” and discuss its main features. In-depth analyses of non-coding RNA biology The main purpose for implementing this web server is to provide biologists with a user-friendly, “one-stop” web tool …

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