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    Books: Human genome textbook
    Submitted by Tore Samuelsson; posted on Wednesday, March 13, 2019

    Submitter

    A textbook with the title "The Human Genome in Health and Disease: A Story of Four Letters" by Tore Samuelsson was recently published by Garland Science / CRC Press. The book explores the intimate link between sequence information and biological function. A range of sequence-based functional units of the genome are discussed and illustrated with inherited disorders and cancer. One chapter is dedicated to sequence bioinformatics.

    The human genome is a linear sequence of roughly 3 billion bases and information regarding this genome is accumulating at an astonishing rate. Inspired by these advances, The Human Genome in Health and Disease: A Story of Four Letters explores the intimate link between sequence information and biological function. A range of sequence-based functional units of the genome are discussed and illustrated with inherited disorders and cancer. In addition, the book considers valuable medical applications related to human genome sequencing, such as gene therapy methods and the identification of causative mutations in rare genetic disorders.

    The primary audiences of the book are students of genetics, biology, medicine, molecular biology and bioinformatics. Richly illustrated with review questions provided for each chapter, the book helps students without previous studies of genetics and molecular biology. It may also be of benefit for advanced non-academics, which in the era of personal genomics, want to learn more about their genome.

    AVAILABILITY

    www.amazon.com/Huma[...]5917/ and bddy.me/2XvX2WQ

    Submitter

    August 12-16, 2019 (Monday-Friday)
    University of Washington Campus, Seattle, WA, USA
    uwcmg.org/docs[...]n.pdf

    The University of Washington Center for Mendelian Genomics (UW-CMG) offers is offering a weeklong course on the analysis of next generation sequence data that will focus on strategies and tools for solving rare Mendelian disorders. The course is intended for data analysts and researchers who analyze next‐generation sequence data.

    We are currently accepting applications for this year's course

    Lunch and snacks provided, on-campus housing available.

    A laptop and specific software are required for participation.

    The course will consist of lectures and hands-on exercises designed to help reinforce the lecture content.

    Monday: IT infrastructure, pipeline overview, CMG data, VCF files and Unix basics
    Tuesday: QC, study design & modes of analysis
    Wednesday: Annotation, interpreting CNV results, introduction to Gemini, and analysis using Gemini for de novo model
    Thursday: Analysis using Gemini for autosomal recessive and autosomal dominant models, candidate genes and variants, and hands-on exercises
    Friday: Team and challenge projects using real-world data, presentations, wrap up, additional questions, and feedback

    For more information and to download a workshop flyer and application, please see the PDF.
    Resources: New NCI Data Science and Informatics Website
    Submitted by Jordan; posted on Thursday, March 07, 2019

    The National Cancer Institute's (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) is excited to announce the launch of datascience.cancer.gov, a new website for data science and informatics resources!

    Replacing CBIIT's former public site, datascience.cancer.gov has a wide variety of resources, including: data sets, data sharing policies and guidance, NCI Cloud Resources, and more.

    Bookmark the new datascience.cancer.gov website and follow NCI CBIIT on Twitter @NCIDataSci and on the NCI Cancer Data Science LinkedIn group for the latest NCI data science news and updates.

    April 23-26, 2019
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    faes.org/biotech87

    OBJECTIVES

    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.

    BACKGROUND

    Computer programs are meant to perform repeated, monotonous, fast, reproducible tasks, handling any amount of data. Researchers often come across situations where existingprograms don't suit their needs. In the era of BigData, without the ability to quickly put together aprogram that would solve their problem, researchers face a road block that is not efficientlysolvable by a human.This training will walk through participants in writing programs that wouldhelp them solve their own problems.

    HIGHLIGHTS

    • 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.

    Submitter

    ccPDB 2.0 (webs.iiitd.edu.in/raghava/ccpdb) is an updated version of the manually curated database ccPDB that maintains datasets required for developing methods to predict the structure and function of proteins. The number of datasets compiled from literature increased from 45 to 141 in ccPDB 2.0. Similarly, the number of protein structures used for creating datasets also increased from ~74 000 to ~137 000 (PDB March 2018 release).

    AVAILABILITY

    URL of resource: webs.iiitd.edu.in/raghava/ccpdb/

    ARTICLE

    Paper URL: www.ncbi.nlm.nih.gov/pmc/[...]3045/
    Education: Training in Computational Drug Design and Discovery @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Thursday, February 07, 2019

    April 9-12, 2019
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    faes.org/biotech66April

    OBJECTIVES

    This hands-on training will introduce researchers to the concepts, methods and tools for structure and ligand based computational drug designing and discovery using the open source tools and the cloud computing facilities.

    BACKGROUND

    Computational drug design and discovery has been a challenging task due to limitations in available computing resources. Public cloud computing facilities have dramatically changed this scenario, by bringing the most powerful computing systems within a click away, with unprecedented low cost options.

    HANDS-ON SKILLS & TOOLS TAUGHT

    • Ligand preparation: OpenBabel
    • Target preparation: Chimera
    • Databases: ZINC, PubChem, ChemSpider, ChEMBL, DrugBank, Binding DB
    • Docking: AutoDockTools
    • Visualization: Chimera, PyMOL
    • Structure based virtual screening: AutoDock, Dock
    • Ligand drawing & visualization: Chemdraw, Chemsketch
    • Compound library: ChemT (or DRUGSTER or FSees)
    • Descriptors: Mold2
    • QSAR: Open3DQSAR (or TEST or Coral)
    • Pharmacophore exploration: Open3DQSAR (or DRUGON or pharmacophore)
    • Ligand alignment: LIGSIFT
    • Ligand based virtual screening: LIGSIFT (or MOLA or lisica)
    • ADMET, Toxicity estimation: Toxtree (or DataWarrior)

    HIGHLIGHTS

    • Cloud-based, high performance computing platform
    • Cloud image freely provided to participants
    • Training provided by active NIH researchers
    • Cookbook style bound manual for all exercises
    • Direct, after training support through exclusive forum membership
    • Continuing Educational Credits
    Etc.: Ranking of countries & institutes
    Submitted by Gajendra P.S. Raghava; posted on Wednesday, January 30, 2019

    Submitter

    An updated ranking of institutes and countries based on developed biological databases is available at bigd.big.ac.cn/data[...]/stat. India is maintaining fourth position, and the Institute of Microbial Technology, Chandigarh is in the third position (after EBI and NCBI). This is a big achievement for any institute to reach third position in the world.

    Submitter

    March 11-15, 2019
    Free University of Berlin, Germany
    www.physalia-courses.org/cour[...]se32/

    Our instructor for this course is Dr. January Weiner (Staff Scientist at the Max Planck Institute for Infection Biology, Germany).

    Registration deadline: February 10th. We have a limited number of places available for this course.

    This course offers computational techniques that go beyond a simple technical or statistical analysis. It covers techniques for the analysis of gene set enrichments, pathway analysis, gene ontologies, functional analysis of metabolomic profiling and making use of correlations and coexpression networks. A prominent part of the course will be devoted to data visualization and visual data exploration.

    The students will gain the ability to independently process and analyse HT data sets, select the appropriate tools, functionally interpret the results as well as learn the paradigms of computational biology and statistics which will allow them to efficiently communicate with computational biologists.

    As an incentive, each student will receive a set of gene expression profiles for a different organism, and during the course they will use these to generate species-specific gene expression modules and test their utility. If we are successfull, we will attempt a joint publication.

    For more information about the course, please visit the course website.

    Here you can find the complete list of our courses and Workshops: www.physalia-courses.org/courses-workshops/

    Should you have any questions, please feel free to contact us at: info[at]physalia-courses.org
    Events: Photonex Glasgow -- Conference and Exhibition 2019
    Submitted by Brenda Hargreaves; posted on Friday, January 18, 2019

    June 5, 2019
    Technology and Information Centre, University of Strathclyde
    Glasgow, United Kingdom
    www.photonexroadshow.com

    Significant advances in photonics are leading to an ever increasing role in the biomedical, chemical and life sciences, in medicine, clinical sciences, neurophysiology, etc.

    The conference aim is to fire your imagination. Whilst it will address advances in imaging, biomedical spectroscopy, quantitative imaging, super resolution microscopy and other topical subjects, the conference will also examine the application of biophotonic devices for global health. It will look at real-world clinical applications and new diagnostic uses, the deployment and the translation of optical sciences and light based technologies.

    This is the sixth conference which changes venue from year to year and will be held at University of Strathclyde this year on Wednesday 5th June 2019.

    The conference programme comprises presentations by invited speakers from academia and selected professional updates from industry. There will be a poster session of contributed papers from early career scientists who are researching novel and exciting new techniques or unique applications.

    What else is going on:
    There is an exhibition of 25 companies dedicated to optical components instruments, imaging, lasers, optoelectronics, sensing technologies, tools and techniques. You can view latest photonics applications and solutions.

    Photonics is an enabling technology – exhibitors develop solutions to satisfy your applications and it is only face-to-face that you can really find out how a company can help you in your work. For further details, please visit our website.

    Submitter

    There was a recent blog post from Semantic Scholar - a competitor to Google Scholar - where they found the most-mentioned GitHub repos in the biomedical literature. They extracted the URLs for the repos from the body text of the papers. The blog post is at blog.semanticscholar.org/top-[...]1930a

    Full disclosure: I work on the Semantic Scholar project and was the one who wrote the blog post. It's pretty cool because we looked at the top repos mentioned by any biomedical paper in our corpus, but it turned out that almost everything was bioinformatics rather than other areas of biology.
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