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    Awards: Benjamin Franklin Award nominees
    Submitted by J.W. Bizzaro; posted on Thursday, February 20, 2020

    Submitter

    There are 13 (!) scientists on the ballot for the Benjamin Franklin Award this year:
    • Amos Bairoch, University of Geneva and Swiss Institute of Bioinformatics
    • Keith A. Crandall, George Washington University
    • Chris Dagdigian, BioTeam
    • Xiaole Shirley Liu, Dana-Farber Cancer Institute
    • Maria Nattestad, Google Health
    • Christine Orengo, University College London
    • B.F. Francis Ouellette, Bioinformatics.ca
    • Aviv Regev, Broad Institute
    • Knut Reinert, Freie Universität Berlin
    • Mark Robinson, University of Zurich and Swiss Institute of Bioinformatics
    • Susanna Sansone, University of Oxford
    • John D., Westbrook, RCSB Protein Data Bank
    • Nadine Ziemert, Universität Tübingen
    Register for free (if you aren't already) and vote: bioinformatics.org/franklin/. Voting will be open until Friday, February 28. The winner will receive the award at the 2020 Bio-IT World Conference & Expo: www.bio-itworldexpo.com.

    Bio-IT World posted an article with additional information on each of the nominees: www.bio-itworld.com/2020[...].aspx.
    Education: Free data science courses ranked by user reviews
    Submitted by neolk roberts; posted on Thursday, February 20, 2020

    I wanted to introduce a list of free aggregated data science courses: www.courseduck.com/prog[...]ence/.

    The courses are primarily for beginner and intermediate developers, and all of them can be taken online. It's a good mix of university courses, courses from various independent providers, and YouTube playlists.

    Course duration is listed for each course, which is convenient because this information can be tough to find. You can also find student reviews available for most courses as well as the major PRO's and CON's of each course.

    Course suggestions and feedback can be submitted here: www.courseduck.com/contact-us/.

    Submitter

    We are happy to announce a new repository of web services developed by the Indian community. This repository maintains information about more than 550 freely accessible functional resources that include around 263 biological databases. Each entry provides complete details about a resource, including the name of resource, web link, details of the publication, information about the corresponding author, name of institute, and type of resource.

    AVAILABILITY

    Web server: webs.iiitd.edu.in/raghava/indiabiodb/
    Mobil App: androidappsapk.co/detail-indiabiodb/

    ARTICLE

    Paper link: www.biorxiv.org/cont[...]627v1
    Awards: Bioinformatics.org to form a steering committee for the Benjamin Franklin Award
    Submitted by J.W. Bizzaro; posted on Tuesday, January 28, 2020 (1 comment)

    Submitter

    Bioinformatics.org has been an important part of the bioinformatics community since 1998. The organization hosts hundreds of applications, databases, educational materials, and other resources. Our more than 40,000 members worldwide participate by sharing these resources, including community news and career opportunities. Among the offerings from Bioinformatics.org is an annual award recognizing advancements and contributions in open science. The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by Bioinformatics.org to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. The award was born out of a desire to recognize work contributing to openness in science by J.W. Bizzaro, founder of Bioinformatics.org.

    The organizers of Bioinformatics.org are committed to recognizing the achievements of the diverse bioinformatics community, including the important contributions of women and minorities to the field of bioinformatics and – in particular – the open resources that drive it.

    To improve our ability to do that, Bioinformatics.org will form and convene a steering committee to bring new advice and voices to the table as we further improve the awards system for the future. The committee will specifically address the representation of women and minorities in the selection process, and will be made up of scientists from outside of Bioinformatics.org.

    Starting today, Bioinformatics.org will make the following changes to the Franklin Award nomination process:
    • One will not need to join Bioinformatics.org or any other organization in order to nominate someone for the award (but free registration will remain a requirement for voting on the ballot).
    • There will be no limit to the number of nominations that an individual can submit (but each nomination will still need to meet the basic criteria described on the page about the selection process).
    There are many deserving scientists in our space, and it is our hope that these expanded nomination criteria will raise more names for consideration.

    For more information on the award and the selection process, please visit www.bioinformatics.org/franklin/.

    Submitter

    Although women have made many groundbreaking advances in the natural and computational sciences in recent years, e.g. Jennifer Doudna and Emmanuelle Charpentier in the development of CRISPR-mediated genome editing, very few have been recognized with top awards. For example, in the 2010s, only one Nobel Prize in Physiology or Medicine was given to a woman (en.wikipedia.org/wiki[...]eates). That's out of 25 winners. In the same decade, only one out of 27 Nobel Prizes in Chemistry was given to a woman.

    Also in the last decade, only one woman received the A.M. Turing Award in computer science (amturing.acm.org/byyear.cfm). And that's out of 14 winners.

    The Benjamin Franklin Award, although not of the same stature as the Nobel or Turing, has been no different. In the past 18 years, only one of the winners has been a woman (www.bioinformatics.org/franklin/). We acknowledge that and would like to see a greater representation of women going forward.

    Last week I was interviewed by Bio-IT World about the purpose of the award, the process, and our need to address the issue of diversity: www.bio-itworld.com/2020[...].aspx

    To those who believe the open process is to blame, it is important to note that the Nobel Prize uses a completely closed process, and the Turing Prize only accepts nominations, not votes. It is very important to us at Bioinformatics.org that the Franklin Award be given to someone selected by the community. It has always been the People's Choice Award for open access in the life sciences. But we need greater participation in the nomination process from the community in order to address the issue.

    During the 2020 nomination period, we will provide (via email) a list of people who have been nominated at least once. We think that once recognizable names are seen, seconding will soon follow. And anyone who has received two nominations that meet the basic criteria (www.bioinformatics.org/fran[...]n.php) will be placed on a ballot for membership vote.

    Submit your nomination today: www.bioinformatics.org/franklin/nominate/

    Submitter

    March 25-27, 2020
    Munich, Germany
    www.ecseq.com/work[...]ction

    Advance your research. Understand NGS and analyze sequenced data yourself.

    IN A NUTSHELL

    • Learn the essential computing skills for NGS bioinformatics
    • Understand NGS technology, algorithms and data formats
    • Use bioinformatics tools for handling sequencing data
    • Perform first downstream analyses for studying genetic variation

    SCOPE AND TOPICS

    The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina.

    All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.

    Check our new course layout: www.ecseq.com/work[...]ction

    Submitter

    April 22-24, 2020
    Brno, Czech Republic
    www.seqme.eu/en/c[...]nners

    Nowadays, Next-Generation sequencing technologies form an essential part of almost all disciplines of biological sciences in research and diagnostics. Due to their quantity and namely complexity, NGS data are typically processed by qualified bioinformaticians or computational biologists. This presents a serious issue even for experienced researchers who have never studied this field of science simply because it has emerged just recently and suddenly there is a need to adapt to completely new tools, workflows and scientific terminology not to perform this sequencing data analysis process – after all, this is why we employ bioinformaticians, but to understand it properly.

    Our workshop gives you the opportunity to understand basics of NGS data processing. The aim of the workshop is to teach you to perform basic steps of NGS data analysis including but not limited to raw data manipulations, quality control, removal of low-quality sequences, sequencing adapters, artifacts, or other contaminations, and especially preparation of a high-quality data set that can be used for downstream analysis.

    You will get to know various NGS data formats, learn about specific problems of sequencing technologies used and how to handle them, and understand the background of individual processes in NGS data editing. You will not become a bioinformatician after this 3-day workshop, but you will set off for becoming a qualified partner for bioinformaticians in your team.

    Please note: If you are not familiar with Next-Generation sequencing technologies, we do encourage you to take part also at our 2-day Introduction to Next-Generation Sequencing Course, which is just preceding this workshop.

    Who should attend?
    This workshop is designed for biologists or beginners in bioinformatics who perform or plan to perform Next-Generation sequencing data analysis. No prior knowledge of sequence data analysis or specific programming skills are required.

    You will learn to:
    • Work in a command line in Ubuntu Unix operating system environment
    • Evaluate quality of raw NGS data
    • Perform basic operations with NGS data
    • Remove low-quality reads, sequencing artifacts, duplications and contaminations
    • Visualize results
    • You will have the option of networking with experienced team of speakers and other participants
    Overall, you will learn all essential steps how to prepare NGS data for advanced downstream analysis (application-specific).

    Submitter

    EXCERPT

    Researchers at the Crick, UCLA Jonsson Comprehensive Cancer Center, Oregon Health & Science University, the Oxford Big Data Institute, and the University of Toronto have created new open-source software which determines the accuracy of computer predictions of genetic variation within tumour samples.
    Source: www.crick.ac.uk/news[...]etics

    ARTICLE

    dx.doi.org/10.1[...]364-z

    Submitter

    EXCERPT

    Online services that allow users to upload their genetic information, research genealogy and find lost relatives may be vulnerable to a sort of genetic hacking, according to two geneticists at the University of California, Davis. A paper describing the work is published Jan. 7 in the journal eLife.
    Source: medicalxpress.com/news[...].html

    ARTICLE

    dx.doi.org/10.7554/eLife.51810
    Education: Physalia courses in 2020
    Submitted by Carlo Pecoraro; posted on Tuesday, December 31, 2019

    Submitter

    See you in Berlin with a mix of "old" and "new" courses and an amazing lineup of instructors: physalia-courses.org/courses-workshops/
    • Advanced Programming in R
    • Bayesian data analysis
    • Bioinformatics Workflows with Nextflow
    • DataViz in R with ggplot2
    • Ecological niche models in R
    • Eukaryotic Metabarcoding
    • Genome Assembly Using Oxford Nanopore Sequencing
    • Geometric Morphometrics
    • Introduction to GWAS
    • Introduction to statistics in R
    • Landscape Genomics
    • Mapping and spatial analysis (GIS) with R
    • Metabarcoding in Spanish
    • Metabarcoding of microbial communities
    • Metagenomics, metatranscriptomics, and multi'omics for microbial community studies
    • Phylogenomics
    • Population Genomics
    • Proteomics using R/Bioconductor
    • RADseq data analysis
    • Single Cell RNAseq
    • Speciation Genomics
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    Acknowledgments

    We wish to thank the following for their support:

    [UW-Platteville]
    [Bio-IT World]
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