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    Education: Training in Bioinformatics for Beginners @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Monday, March 19, 2018

    April 17-20, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA[...]p;ch=


    Bioinformatics (Computational Biology) is a must skill required in every modern biomedical research lab. Installing and configuring a wide variety of computational biology tools is a cumbersome task that requires software engineering skills. This hands-on training course will introduce participants to a custom, all-in-one, fully loaded linux desktop (with windows like graphical user interface) machine, that comes with hundreds of popular computational biology (bioinformatics) tools required for a successful modern biomedical research lab.


    The participants will be provided with end-to-end hands-on training, along with introduction tobasic concepts, in using popular tools and techniques for sequence analysis, structure analysis, function prediction, biological database searching, "omics" data analysis, pathway analysis, datavisualization, data curation and integration, linux, R, perl and scripting basics.rticipants should be comfortable with basic computer skills.

    Hands-on Skills/Tools Taught:
    • Databases: NCBI-ENTREZ, UniProt, PDB, STRING, Others.
    • Sequence analysis and function predictions: EMBOSS suite & others
    • Local Alignment: EMBOSS-WATER
    • Global Alignment: EMBOSS-NEEDLE
    • Similarity search: NCBI BLAST, PSI-BLAST
    • Multiple sequence alignment: Clustal Omega, MUSCLE, MAFFT
    • Phylogenetics: MrBayes, MEGA, FigTree and Dendroscope
    • Motif finding, analysis: MEME suite
    • Structure prediction, visualization & analysis: PyMOL, Chimera, iTASSER
    • Transcriptome analysis: NCBI GEO, Tuxedo tools, R
    • Enrichment analysis: DAVID
    • Pathway analysis: Cytoscape
    • Programming: R, Perl, Python
    • Platforms: EMBOSS, UGENE, H2O, Galaxy
    Awards: Announcing the 2018 Benjamin Franklin Award laureate
    Submitted by J.W. Bizzaro; posted on Thursday, March 15, 2018


    We are happy to announce that the members of have chosen by vote Desmond Higgins of the University College Dublin (UCD) Conway Institute as the laureate of the 2018 Benjamin Franklin Award for Open Access in the Life Sciences!

    The Higgins lab has developed the CLUSTAL series of multiple sequence alignment tools, which are among the very first bioinformatics tools used by any student and are fundamental to the field, so it's very much an honor for us to recognize Des for his contribution.

    The ceremony will take place on May 17th at the Bio-IT World Conference & Expo ( in Boston, Massachusetts. We hope to see you there!
    Education: FORCE11 Scholarly Communication Institute (FSCI)
    Submitted by Suzi Smith; posted on Monday, March 05, 2018

    July 30 - August 3, 2018
    University of California San Diego (UCSD), La Jolla, CA, USA

    The FORCE11 Scholarly Communications Institute at the University of California, San Diego is a week long summer training course, incorporating intensive coursework, seminar participation, group activities, lectures and hands-on training. Participants will attend courses taught by world-wide leading experts in scholarly communications. Participants will also have the opportunity to discuss the latest trends and gain expertise in new technologies in research flow, new forms of publication, new standards and expectations, and new ways of measuring and demonstrating success that are transforming science and scholarship.
    Awards: Nominees for the 2018 Benjamin Franklin Award
    Submitted by J.W. Bizzaro; posted on Monday, March 05, 2018


    We're happy to announce the nominees for the 2018 Benjamin Franklin Award for Open Access in the Life Sciences, as selected by our members: Members may vote online at We'll also send out an email ballot in short order.

    The award ceremony will take place on May 17 at the 2018 Bio-IT World Conference & Expo:

    May 15-17, 2018
    World Trade Center, Boston, Massachusetts

    There's been dramatic progress in life science technologies over the years, yet the fundamental goal of the Bio-IT community remains the same – to make the most of data and computing to advance medicine. Since 2002, Bio-IT World has played an integral role in this, bringing together clever, innovative people from all areas of life sciences for expert commentary and industry insight. Our 2017 event brought together more than 3,400 attendees from 35 countries to make connections and forge collaborations across the life sciences. This year promises to be even better. With 16 tracks, 14 pre-conference workshops, and three industry awards, the 2018 Bio-IT World Conference & Expo will offer more opportunities to build the relationships that drive the Bio-IT industry forward.
    Resources: AntiTbPdb: A knowledgebase of anti-tubercular peptides
    Submitted by Gajendra Raghava; posted on Thursday, March 01, 2018


    We are pleased to announce a new database of anti-tubecular peptides from our group.



    April 9-13, 2018
    Berlin, Germany[...]se33/

    This course will provide a thorough introduction to microbial community data analysis (metagenomics, metatranscriptomics, and other culture-independent molecular data) through a balanced approach of lectures and hands-on lab sessions. Course participants will learn how to process data from raw meta'omic sequencing files through appropriate bioinformatic methods and approaches for subsequent integrative statistical analyses. Participants are invited to bring their own data to the practical session on the final day or can use publicly available data from the Integrative Human Microbiome Project (HMP2).

    Dr. Curtis Huttenhower (Harvard School of Public Health, USA)
    Dr. Melanie Schirmer (The Broad Institute of MIT & Harvard, USA)
    Dr. Kevin Bonham (The Broad Institute of MIT & Harvard, USA)

    For more information, please visit our website.
    Resources: A web server for predicting antifungal peptides
    Submitted by Gajendra Raghava; posted on Monday, February 26, 2018



    Events: Definiens International Symposium on Tissue Phenomics
    Submitted by Colleen Craig; posted on Thursday, February 22, 2018

    April 24-25, 2018
    Hotel Marlowe, Cambridge, MA, USA

    You're Invited: Please join us for the Definiens International Symposium for Tissue Phenomics.

    This Symposium advances innovation in translational immuno-oncology, and features diverse perspectives from visionaries who drive the field in the early stages of discovery to transform healthcare through the integration of digital science and medical Big Data.

    Topics discussed will include:
    • 20 years of Artificial Intelligence
    • Immuno-Profiling and Biomarkers
    • Generating Biological Insights
    • Big Data Integration
    • Translating Science into Development
    • Digital Pathology for Patient Care
    Join the conversation with these thought leaders:
    • Simone Bianco, PhD, Research Staff Member, IBM Almaden Research Center
    • Bernie Fox, Ph.D. Chief, Laboratory of Molecular and Tumor Immunology, EACRI, Associate Professor, MMI and Env and Biomolec systems; Leader, Tumor Immunology Focus Group, OHSU Cancer Inst., Oregon Health Science University
    • Pam Ohashi, Ph.D. Director, Tumor Immunotherapy Program, Princess Margaret Cancer Centre
    • Elfriede Noessner, Research Scientist, Institute of Molecular Immunology, Helmholtz Institute, Munich
    • Julien Adam, IGR Paris
    • James Gulley, MD, PhD, Director of the Medical Oncology Service, Office of the Clinical Director, National Cancer Institute
    • Famke Aeffner, Principal Pathologist; Comparative Biology and Safety Sciences; Amgen Inc
    • Robert Kinders, Head of the Pharmacodynamics assay development (PADIS) laboratory, Frederick National Laboratory, National Institute of Health
    • Holger Moch, MD, Professor, Institut für Pathologie und Molekularpathologie, University of Zurich
    • Chris Heery, MD, Chief Medical Officer, Bavarian Nordic
    • Kenneth Lacovara, Explorer / Paleontologist / Author
    • Chandra Saravanan, Senior Veterinary Pathologist, Novartis Institutes for BioMedical Research, Novartis
    • David Rimm, MD, Professor in the Departments of Pathology and Medicine (Oncology); Director of Yale Pathology Tissue Service, Yale University School of Medicine
    • Dirk Jaeger, MD, Professor, University of Heidelberg
    • David Harrison, John Reid Chair of Pathology, Director of Research & Director of Laboratory Medicine, University of St. Andrew
    • Ralf Huss, Chief Medical Officer, Definiens
    • Thomas Heydler, Chief Executive Officer, Definiens
    And many more.

    May 23-25, 2018
    Bologna, Italy

    The workshop intends to present the state-of-the-art of the computational tools for interpreting at the molecular level the effects that genome variations induce in the cell system, contributing to fill the knowledge gap between genotype and phenotype.

    NGS techniques allow detection of the differences in genetic sequences and in gene expression that can be associated to different phenotypes, and statistical methods can estimate a significance level for each association. However, the exploitation of genetic association data requires elucidation of how variations affect the structure of macromolecules and their interaction patterns and how biological processes and pathways are hampered. Proteins, their stability and their relationships in interactomes will be the central topic. Furthermore, a particular regard will be given to the regulation at the transcriptional and translational levels, as derived from epigenomic and ribosome profiling data.

    Computational tools are absolutely necessary to perform the analysis of massive amounts of biomedical data and modern techniques for database integration, non parametric statistics, machine-learning and in particular deep-learning approaches, can have a huge impact in the field. The exploitation of data in the applicative domains, and in particular in translational and stratified medicine, strongly rely on the availability of computational methods able to extract, elaborate and generalise biologically relevant information

    The workshop aims at presenting the state-of-the-art of computational methods for genome interpretation and collects expert scientists from both experimental biomedicine and computational biology. The mixing of competences is fundamental for generating significant advancements, and the proposed workshop .

    The format of the workshop allows extensive interaction among students and lecturers, and offers to young researchers the possibility of presenting their work at poster sessions and with short selected talks.


    Application deadline: April 15, 2018
    Deadline for applying to FEBS Youth Travel Funds (YTF): February 28, 2018

    Two microbiome challenges launched this week with a common goal: evaluate and advance the ability of computational methods to accurately detect known microbial strains in metagenomic samples.

    Both Challenges are great opportunities for the community to come together to advance research and for members in this group to test out their microbiome tools.

    The CFSAN Pathogen Detection Challenge, hosted by precisionFDA, asks participants to develop and use bioinformatics pipelines to identify the types and distribution of Salmonella strains in each of several metagenomics samples. This type of technology will expedite determining the source of foodborne illness. As the food safety community moves to metagenomic sequencing, bioinformatics algorithms must be developed to detect pathogens amongst a mix of organisms sequenced directly from a sample. This Challenge was designed as the first step towards this goal.

    The Mosaic Community Challenge: Strains #2, hosted by Janssen Research & Development, LLC, aims to speed the translation of microbiome science into novel products by tracking the presence of certain known strains in a sample. It is critical to accurately determine the type and quantity of microbes in a sample at the strain-level in order to bring safe and effective products to market, and to precisely monitor their status within the human body. Insights from the Challenge will provide an objective comparison of the performance of different tools. Participants can submit multiple entries and see immediate results of their performance throughout the Challenge using the Mosaic Platform.

    Join us today to get started! Access both Challenges at
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