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    Submitter

    Allison Proffitt at Bio-IT World is compiling a list of organizations that are providing free use of their resources to scientists involved in coronavirus research: www.bio-itworld.com/2020[...].aspx.

    Submitter

    May 18-22, 2020
    Free University (FU) Berlin, Germany
    www.physalia-courses.org/cour[...]rse9/

    INSTRUCTORS

    Dr. Martin Taylor and Dr. Lewis Spurgin (University of East Anglia, UK)

    COURSE OVERVIEW

    Next generation sequencing has revolutionized evolutionary biology allowing unprecedented resolution and insight into evolutionary questions that appeared intractable only a few years ago. The course will cover the basics of population genomic analysis from SNP data onwards and will cover the key analyses that may be required to successfully analyze a population genetic data set. The course will NOT cover steps prior to generation of a .vcf file or SNP data set such as NGS data demultiplexing, clustering and SNP calling (This is covered in detail in the Introduction to RADseq course). This course will introduce Linux and the command line environment, basic perl and python usage, file conversions and manipulation, population structure and differentiation in R, outlier analysis, landscape / seascape genomics and introgression. Having completed the course, students should have a good understanding of the software and methods available for population genomic analysis and be competent in population genomic analysis.

    TARGETED AUDIENCE & ASSUMED BACKGROUND

    This course is aimed at postgraduate students and early career researchers who are interested in using population genomic tools in their research. No previous experience of bioinformatics is required, but an underpinning in evolutionary biology and basic population genetics concepts such as Hardy Weinberg Equilibrium and FST are desirable. The course will use a range of software including the Linux operating system and R.

    Program: www.physalia-courses.org/cour[...]lum9/

    Here is the full list of our courses and Workshops: www.physalia-courses.org/courses-workshops/

    Submitter

    We are in the process of creating computational resources for the novel coronavirus illness (COVID-19) to fight against this deadly infectious disease. We need the help of the community in compiling information and keeping this resource up-to-date. Please visit the following site for comprehensive information on COVID-19: webs.iiitd.edu.in/raghava/coronavir/.
    Education: 4th Berlin Summer School in NGS Data Analysis
    Submitted by Dr. David Langenberger; posted on Wednesday, February 26, 2020

    Submitter

    June 15-19, 2020
    Berlin, Germany
    ecseq.com/summer-school

    IN A NUTSHELL

    • Learn the essential computing skills for NGS bioinformatics
    • Understand NGS analysis algorithms (e.g. read alignment) and data formats
    • Use bioinformatics tools for handling NGS data
    • Perform first downstream analyses for studying genetic variation
    • Compare different approaches for differential expression analysis

    SCOPE & TOPICS

    The purpose of this intense one week summer course is to get a deep 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. You will be trained on understanding NGS data formats and handling potential problems/errors therein. In the summer school we will use a real-life RNA-seq dataset from the current market leader Illumina.

    All students will be enabled to perform important first tasks of NGS data analysis themselves. The layout of the summer school 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.

    In the evenings there will be social events, like a conference dinner, or a guided city tour through Berlin. These are always great networking possibilities.
    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
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    Acknowledgments

    We wish to thank the following for their support:

    [UW-Platteville]
    [Bio-IT World]
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