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    Education: Book and online course: Biostar Handbook
    Submitted by Steven Allford; posted on Wednesday, January 17, 2018



    The answers to some of the greatest questions of life lie within ourselves. Bioinformatics is the new science created by fusing Biology and Data Science.

    Since its release at the end of 2016, the Biostar Handbook has been continuously expanded, improved, and enriched to become one of the most comprehensive and systematic presentations of Bioinformatics from a Data Science perspective:

    Since its release, the book has been adopted across the globe in several universities and research centers. In addition, over the course of the last year, the Biostar Handbook has been expanded with several new chapters covering Metagenomics and ChIP-Seq analysis.

    With the help of the e-book, readers are able to reproduce analytics results from realistic, and cutting-edge data analysis scenarios such as genome variation, SNP calling, genome assembly and RNA-Seq based gene expression studies:

    In the Fall of 2017 an online Bioinformatics Course titled "Learn Bioinformatics in 100 hours" has been added to the book and made available to the readers free of charge:

    The online course provides a structured path through the book and includes assignments and thorough tests and evaluations.

    The Biostar Handbook is the most affordable, low-cost option to get introduced to this new scientific domain. Join the thousands of readers, hundreds of enrolled students that are currently progressing through the book. With the help of the Biostar Handbook, you too can connect to the new generation of scientists that are well prepared to handle the challenges of the data-centric life sciences.
    Education: Variant Analysis at NIH
    Submitted by Vijayaraj Nagarajan; posted on Wednesday, January 10, 2018

    February 27 - March 2, 2018
    National Institutes of Health
    9000 Rockville Pike
    Bethesda, MD, USA


    Next generation sequencing technologies have made genotyping a day to day research and diagnostic tool. Genotyping has come all the way from bench-to-bedside. Genetic variants are being used in personalized medicine to identify susceptibility genes, common disease variants and mutations relevant for diagnosis and therapy.


    Participants will use popular open source tools and techniques necessary for analysing variants starting from raw data quality control. Apart from the regular analysis like alignment, variant calling and annotation, this training will walk through participants in several advanced variant analysis methods and techniques.

    • NGS Basics, experimental design, data format
    • Data quality control, preprocessing and alignment
    • Germline variant calling
    • Somatic variant calling
    • Variant score recalibration and filtering
    • Variant calling best practices
    • Indels, structural and copy-number variation
    • Cohort and population scale analysis
    • Recombination, linkage, LOH, haplotype, allelic imbalance
    • Variant annotation and association analysis
    • Co-variation, causal variation, network analysis

    February 6-9, 2018
    National Institutes of Health
    9000 Rockville Pike
    Bethesda, MD, USA[...]hop-1


    This course will introduce students to bioinformatic analysis of next generation sequencing data, particularly for DNA-seq, RNA-seq, CHIP-seq, and epigenomics. The course will be comprised of lectures and hand-on sessions. Lectures will cover background knowledge and survey various software programs. For hand-on sessions, command line tools will be presented and the galaxy web based platform will be used to analyze primary data. Cloud computing, genomic databases, and de novo assembly will be surveyed.

    • Overview on Bioinformatics Tools: Galaxy (Pre-processing, Format Conversion, etc.)
    • Databases and Tools, SNP Callers, Cloud
    • RNA-seq
    • CHIP-seq
    • Epigenomics
    • Cloud Computing
    • 10k Genomes
    • Data Visualization
    • Comparative Genomics and Genome Alignment (biology + software)
    • Tutorial & Laboratory for de novo Assembly
    • RNA-seq, DNA-sequencing.



    In an effort to vault genetics into a new era of big data, six drug companies say they will decode the genes of half a million Brits and then make the data public – all by 2020.

    The plan will turn the UK Biobank, the source of the DNA samples, into the world's single biggest concentration of genetic and health data anywhere, giving scientists and drug companies a powerful tool for understanding diseases.


    June 10-12, 2018
    Los Angeles, CA, USA

    The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018, will be held on June 10-12, 2018 in Los Angeles, California, USA. The purpose of the ICIBM is to bring together eminent scholars with expertise in various fields of computational biology, systems biology, computational medicine, as well as experimentalists interested in application of computational methods in biomedical studies.

    You are invited to submit abstracts with unpublished original work describing recent advances on all aspects of bioinformatics, Systems Biology and intelligent Computing, including but not restricted to the following topics:

    Systems Biology:
    • Mathematical and quantitative models of cellular and multi-cellular systems
    • Modeling and simulation of biological processes, pathways and networks
    • Multi-dimensional omics data integration
    • Metabolomics
    • Synthetic biological systems
    • Applications of systems biology approaches to biomedical studies
    • Self-organization in living systems (cells, organisms, swarms, ecosystems, etc.)
    • Next generation sequencing data analysis, applications, software and tools
    • Genomics and genetics, including integrative and functional genomics and genome evolution
    • Personalized medicine and translational bioinformatics
    • Big data science including storage, analysis, modeling and visualization
    • Proteomics, protein structure prediction, molecular simulation and evolution
    • Drug discovery, design and repurposing
    • Image analysis and processing
    Intelligent Computing:
    • Evolutionary computing, swarm intelligence/optimization, ensemble methods
    • Machine learning, data mining, pattern recognition and knowledge and discovery
    • Natural langue processing, literature mining, semantic ontology and date privacy
    • Neural computing, kernel, methods, feature selection/extraction
    • Manifold learning theory, artificial life and artificial immune systems


    All submitted papers will be peer-reviewed. Selected papers of the registered authors will be published in special issues of several journals, including BMC Genomics, BMC Systems Biology, BMC Bioinformatics, BMC Medical Genomics, BMC Medical Informatics and Decision Making, International Journal of Computational Biology and Drug Design (IJCBDD), and Human Heredity. Authors need to prepare manuscripts in the format of the corresponding journal that they prefer.


    Call for Papers or Oral Presentations: 2017-10-01 through 2018-02-04
    Call for Posters: 2017-10-01 through 2018-03-25
    Event Registration: 2018-01-01 through 2018-06-10
    Early Registration Deadline: 2018-04-30
    Resources: Bioinformatics forum
    Submitted by Rahul Agarwal; posted on Saturday, December 30, 2017

    Please kindly spread the news about this bioinformatics forum, useful for students, researchers and anyone related to bioinformatics and sequencing:


    March 22-23, 2018
    Florence, Italy

    The 7th edition of the New Perspectives in Science Education Conference promotes transnational cooperation and shares good practices in the field of innovation for science education. The New Perspectives in Science Education Conference is also an excellent opportunity for the presentation of previous and current projects in the science field.

    The Call for Papers, within the New Perspective in Science Education Conference, is addressed to teachers, researchers and experts in the field of science education as well as to coordinators of science and training projects.

    Experts in the field of science teaching and learning are therefore invited to submit an abstract of a paper to be presented during the conference. The abstract should be written in English and submitted no later than 15 January 2018 (extended deadline). In order to submit an abstract please visit our website.


    Extended Deadline for submitting abstracts: January 18, 2018
    Notification of Acceptance / Rejection for Abstracts (Deadline 19 December): January 8, 2018
    Notification of Acceptance / Rejection for Abstracts (Deadline 15 January): January 19, 2018
    Deadline for final submission of papers: January 22, 2018
    Dates of the conference: March 22-23, 2018

    There will be three presentation modalities: oral, poster and virtual presentations.

    All accepted papers will be included in the Conference Proceedings published by LibreriaUniversitaria with ISBN and ISSN codes. This publication will be sent to be reviewed for inclusion in SCOPUS ( Papers will also be included in ACADEMIA.EDU ( and Google Scholar.

    For further information, please contact us at the following address: science[at] or visit the New Perspectives in Science Education conference website.
    Events: Converged IT & the Cloud
    Submitted by James Prudhomme; posted on Monday, December 18, 2017

    February 12-14, 2018
    San Francisco, CA[...]Cloud

    Today, IT professionals are challenged with finding solutions to integrate ever-expanding large volumes of data generated at research labs, pharmaceutical companies and medical centers. In order to do this, one must have the compute power, storage solutions, and analytic capability to make the data from disparate sources such as: omics (genomics, proteomics, metabolomics, etc.), imaging, sensors, and more clinically actionable. The Converged IT & the Cloud conference will bring together key leaders in the fields of cloud computing and data management to share case studies and to discuss the challenges and solutions they face in their centers. Overall, this event will offer practical solutions for network engineers, data architects, software engineers, etc. to achieve the goal of personalized medicine.

    Sessions include:
    • Designing the Cloud for Personalized Medicine
    • Data Integration, Analysis and Storage
    • Data Commons
    • Data Storage and Cloud Computing
    • Building a Better Cloud
    • Trends and Future Directions
    Visit our website to view the full agenda, speaker abstracts and register.

    Organized by: Cambridge Healthtech Institute (CHI)
    Events: Bioinformatics for Big Data Conference
    Submitted by James Prudhomme; posted on Friday, December 15, 2017

    February 12-14, 2018
    San Francisco, CA[...]-data

    In the era of precision medicine, enormous amounts of data are being generated from disparate sources, including omics, imaging, sensing and beyond. Today, computational scientists need to develop better tools to manage, integrate and share data to make it clinically actionable.This will showcase how medical centers and the pharma industry are developing such tools and software to meet this goal.

    Sessions include:
    • Bioinformatics in the Practice of Healthcare: From Data to Clinical Action
    • Personalized Medicine Strategies for Clinically Actionable Data
    • Platforms for Exploring Multi-Omic Data
    • Data Commons
    • Target Validation and Indication Expansion
    • Precision Medicine vs. Accurate Medicine: The Need to Understand Real World Medicine and Real World Patients
    Visit our website to view the full agenda, speaker abstracts and to register.

    Organized by: Cambridge Healthtech Institute (CHI)


    When I was doing molecular biology research, I always had difficulty getting an overview of some genes in the vast human genome network. We often search it through Google image for pathway maps or search from antibody companies, but these sources of pathway maps are hardly customized for our genes of interest and were hardly complete for all the pathways that the gene of interest lead to. And so I developed to provide a light-weight, quick tool for researchers to lookup human genome pathways based on their genes of interest.

    It involves 2 modules:

    MODULE 1

    Single gene pathway analysis:

    Given a gene, find the upstream and/or downstream molecular pathways. You may choose the length of pathways to search for.

    For example, if I input Ago2, I will get its upstream and downstream genes graphed as a tree. I may choose how many genes to search for and how many levels down into the molecular pathway. The search algorithm is based on academic reports: the gene interactions that are reported most will come first.

    There is a button below that can generate a list of references from PubMed for all the genes listed.

    MODULE 2

    Pathway enrichment analysis:

    Given a list of genes, find the pathways that connect them. If a gene cannot be connected, it will not be shown in the figure.

    For example, if I ran some PCR in my cell model and found TP53, AKT1, and PIK3R3 were the most significant genes, I would want to know what other genes could be involved. In a quick search on this website I would find how these genes are related in the human genome network, and figure out ERBB3, RB1, PTK2, and PIK3CA may be worth for further investigation.

    Same as single gene pathway analysis, there will also be a button appearing below the graph, which will generate a list of references for you.

    You may notice that some genes are reported repeatedly, so they can generate a long list.

    The database of this website currently is based on BioGrid's open dataset for 1 Dec 2017. I will keep updating when I get new data sources. It currently records 16,760 genes and 369,824 papers.

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