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    Education: Free Webinar: Biomedical Data, Simplified
    Submitted by Sahil Sethi; posted on Friday, October 19, 2018


    Our recent webinar on the critical role data science tools and skills play in the advancement of biomedical research and precision medicine.

    Watch now:

    Announcing the start of an online training program designed to empower researchers, clinicians and students to handle their own high-throughput datasets and extracting insights through processing, analysis, machine learning and visualization. Learn more:
    Resources: Vaccine Against Major Pathogenic Species of Bacteria
    Submitted by Gajendra Raghava; posted on Thursday, October 18, 2018


    We created a web-based resource on predicted vaccine candidates against major pathogens, and we hope these candidates will be utilized by experimental researchers to develop vaccines against bacterial strains responsible for diseases.

    Events: Symposium on Accelerating Biology 2019: Towards Thinking Machines
    Submitted by Ruma Banerjee; posted on Tuesday, September 18, 2018

    February 5-7, 2019
    Indian Institute of Science Education and Research (IISER)
    Dr Homi Bhabha Rd
    Pashan, Pune
    Maharashtra, India[...]y2019

    The Bioinformatics group of C-DAC is organizing a three-day symposium that will include talks by eminent scientists from academia and industry and will address the challenges in the areas of "Personalized medicine, Cognitive computing, Drug design, Big data tools etc." Early bird registration closes on 30 November 2018 and Poster abstracts can be sent in latest by 4th January 2019, 6 pm.

    To avail special discount on group registrations (10 participants and above) kindly contact ab2019[at]

    We encourage participation from students and early-career researchers from diverse fields of microbiology, genetics, biochemistry, bioinformatics, biotechnology, anthropology, geology and other allied fields.


    Any further quires can be directed to:
    Phone: 020-25503272
    Email: ab2019[at]

    Genestack has been working on a transcriptomics tool for the pharma/biotech market in collaboration with Boehringer Ingelheim. In short, it helps biologists interrogate and visualise expression data, at scale, without the support of a bioinformatician. This then allows bioinformaticians to concentrate on things that bring the most benefit to their work. And this is why I'm reaching out to

    We are inviting industry and academic professionals to get 1-month free early access to this tool and help shape its development through user research. To take part, simply book a "User Chat" with a Genestack specialist here:

    Or you can find out more about the tool here:[...]iner/.
    Resources: Prediction of Anti-Tuberculosis Peptides
    Submitted by Gajendra Raghava; posted on Saturday, September 01, 2018


    We are pleased to announce another paper based on web services developed by our group. This server will be useful for researchers working in the field of drug design against tuberculosis.


    Server URL:


    Paper Link:[...]/full

    September 25-28, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA[...]hop-3


    Apart from performing the routine differential expression analysis using two different suite of tools, this hands-on training will help participants learn advanced RNA-Seq analysis techniques and tools for detecting snps, fusion genes, allele specific expressions, circular RNAs, viral/bacterial sequence identification, alternative polyadenylation and transcriptional regulatory network analysis.


    • Participants will use a Graphic User Interface based Linux Desktop environment, specially configured for advanced RNA-Seq analysis in the Amazon Cloud
    • Training provided by experienced active NIH researchers
    • Cookbook style bound manual for all exercises
    • Direct, after training support through exclusive forum membership
    • Continuing Education Credits


    • Differential expression analysis: New Tuxedo tools
    • Differential expression analysis: Trinity tools
    • Fusion gene analysis : STAR-Fusion
    • SNP detection : GATK
    • Allele specific expression : WASP
    • Circular RNA identification : circexplorer
    • Alternative polyadenylation : DaPars
    • Viral integration : VirusFinder
    • Network analysis : Cytoscape

    September 11-14, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA[...]p;d4=


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

    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: Linux, R, Perl, Python
    • Platforms: EMBOSS, UGENE, H2O, Galaxy

    Sunday, September 9, 2018
    Athens, Greece (during ECCB2018)

    Submission deadline for abstracts has been extended until August 15. Travel awards available!

    Digital and computational pathology are increasingly used to study biological processes and diseases as novel molecular probing and imaging techniques allow the measurement of single molecules in whole tissue sections. Resulting multi-gigapixel images can be viewed on a computer screen via dedicated software. However, automated analysis of such large-scale datasets is challenging and their combination with omics data is not trivial. This workshop wants to facilitate bridging opportunities between the bioinformatics and tissue image analysis communities.

    This second edition is organized as a full-day workshop during ECCB 2018 (


    Computational pathology exists at the interphase between bioinformatics, machine learning, and digital pathology (microscopy). Submissions from all topics of interest are welcome (non-exhaustive list):

    Machine learning and image analysis for quantification in digital pathology (in 2D & 3D), Novel approaches (e.g. spatial or graph-based methods) to extract high-level features (e.g. molecular networks or spatial expression patterns) from tissue images for systems pathology, Software development methodologies and tools to ease the exploitation of large tissue images and integration with omics data, Novel molecular imaging techniques on tissues (molecular pathology, next generation pathology) and their analysis challenges, e.g. in situ hybridization, mass spectrometry imaging of formalin-fixed paraffin-embedded tissues, mass cytometry, and other spectroscopy techniques (Raman, ...), ... Research applications on non-human model organisms


    The following keynote speakers are confirmed to speak at the conference:

    Thomas Fuchs, Memorial Sloan Kettering Cancer Center
    Chakra Chennubhotla, University of Pittsburgh
    Derek Magee, University of Leeds


    The conference solicits oral talks, posters, and proceeding papers contributions of original work or work that was recently accepted or published in a peer-reviewed journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review.

    Conference proceedings will be published by the Journal of Pathology Informatics.

    The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session. For submission instructions, please refer to


    Submission deadline: August 15, 2018.
    Conference: Sunday September 9, 2018.


    June 28th, 2018, 4:00 pm to 7:00 pm (Eastern European Time)

    This RNA-seq workshop is perfect for those interested to get more hands-on practice with bioinformatics or to kick-start a project that has been sitting on the shelf, waiting for the right time. In the workshop, participants will have the opportunity to review and start using the T-BioInfo Bioinformatics platform (

    The platform has dedicated sections to analyze Exome-Seq, RNA-Seq, Metagenomics and other "omics" data types. With a visual and intuitive interface that eliminates the need for coding, any clinician or biologist can prepare complex processing pipelines and deploy powerful machine learning algorithms to extract meaningful insights from large datasets. The approaches tested on this platform can be deployed independently and extended in a familiar environment like Excel or R for post-processing. Here is an example of the T-BioInfo platform in action:

    The workshop will address the basics of using the platform for RNA-seq data processing and downstream analysis. We will review bioinformatics concepts relevant to high-throughput data like data processing, exploration, analysis and interpretation. We will primarily focus on RNA seq data like gene/isoform expression, but the same concepts can apply to other types of data.

    After a demonstration of the T-BioInfo platform interface and review of methods in the supervised and unsupervised data mining sections, we will discuss free educational resources and our ongoing or planned pilots where students can gain practical experience and get involved in research opportunities. The platform is in public beta and has a research or educational account types available.

    August 7-10, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA[...]p;d=4


    Participants will get a brief introduction to the programming concepts, followed by hands-on walkthrough for writing scripts using the Unix Shell Programming Language, R, Perl and Python. We will start from reading the data, processing it and all the way until saving the processed data. This training will walk through participants in writing programs that would help them solve their own problems.


    • Participants will work in a Unix environment.
    • Participants will get a copy of all the scripts used in the class.
    • Participants will also receive a cookbook style manual for all the hands-on exercises.
    • After training support is also provided through exclusive members only forum.
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