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Trends in bioinformatics

Choosing the right name for a bioinformatics tool

The name of your bioinformatics tool is the icing on the cake. You should be very attentive and feel concerned regarding this feature. While having a great name does not assure you to stand out, a bad appellation often results in a failure to reach your audience. The do’s and don’ts Don’t take a name that already exists Your tool is unique. As such, it deserves to have a sole name. Don’t try to copy the name of a famous tool or your favorite one. It can be detrimental for you. Indeed, people tend to compare products with each other, especially if they have the same title. They can be confused about the function of your tool.   OMICtools contains …

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qPCR techniques and analysis software tools

Quantitative real-time polymerase chain reaction (qPCR) is widely used for the detection of specific nucleic acids, measurement of RNA transcript abundance and validation of high-throughput experimental results. While high-throughput sequencing (HTS) has revolutionized the fields of genomics and transcriptomics, qPCR techniques have evolved and can now be performed in a high-throughput fashion. Introduction qPCR is an easy-to-perform technique to evaluate the relative (or absolute) expression of genes as compared to each other and/or a reference. Traditional qPCR is often used to validate results from gene arrays or HTS, as it is more precise, rapid to perform, and cheap.   Recently, new technologies have been developed to increase the number of genes that can be tested simultaneously. Next generation qPCR platforms …

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Choose and use the right license for your software tool

Whether you are a software developer wishing to distribute your tool, or a user/programmer in need to use and/or modify a tool, you are confronted to licensing. Software licenses govern the use or redistribution of a software under specific laws. Two common categories for software under copyright law (which grants the licensee specific rights) are proprietary software and free and open source software (FOSS). The main difference between proprietary and FOSS license is the granting of rights to modify and re-use a software by a customer: FOSS software licenses both rights to the customer, while proprietary software does not license these rights (Wikipedia).   Software licenses on OMICtools   Following the general tendency to develop more open-source software, more than …

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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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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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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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How to find bioinformatics jobs

As part of your market strategy, you should craft and maintain a professional online persona. Use a platform such as LinkedIn or ResearchGate to create a detailed profile emphasizing key skills and experience, and to link up with others in relevant organizations or fields of research (…) Use online technical forums to ask about skills and experience needed in an industry  (…) Taking part in such dialogues can make recruiters notice you and seek you out regarding prospective openings. Peter Fiske. Why scientists need to market themselves. Nature.   As a job seeker, you probably use solutions to find job opportunities in your field of expertise. It can be difficult and time consuming to manually vet the many options available …

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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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