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    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.

    Submitter

    June 9-11, 2019
    Columbus, Ohio, USA
    icibm2019.org

    It is our great pleasure to announce the 7th International Conference on Intelligent Biology and Medicine (ICIBM 2019). ICIBM is a high caliber conference which brings 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. The purpose of the ICIBM is to provide a congenial atmosphere highly conducive to extensive discussion and networking.

    CALL FOR PAPERS

    You are invited to submit papers with unpublished original work describing recent advances on all aspects of Bioinformatics, Intelligent Computing, Systems Biology, and Medical Informatics, including but not restricted to the following topics:

    Bioinformatics:
    • Genomics and genetics, including integrative & functional genomics, genome evolution
    • Next generation sequencing data analysis, applications, and software and tools
    • Big data science including storage, analysis, modeling, visualization, and cloud
    • Precision medicine, translational bioinformatics and medical informatics
    • Drug discovery, design, and re-purposing
    • Proteomics, and protein structure prediction, molecular simulation and evolution
    • Single cell sequencing data analysis
    • Microbiome and Metagenomic
    Intelligent Computing:
    • Artificial intelligence, machine learning, deep learning, data mining, knowledge discovery
    • Natural language processing, literature mining, semantic ontology, and health informatics
    • Neural computing, kernel methods, feature selection/extraction
    • Evolutionary computing, swarm intelligence / optimization, ensemble methods
    • Manifold learning theory, artificial life and artificial immune
    • Image analysis and processing
    Systems Biology:
    • Modeling and simulation of biological processes, pathways, and networks
    • Mathematical and quantitative models of cellular and multi-cellular systems
    • Multi-dimensional omics data integration
    • Synthetic biological systems
    • Metabolomics, microbiome, and lipidomics
    • Self-organization in living systems (cells, organisms, swarms, ecosystems, etc.)
    • Applications of systems biology approaches to biomedical studies
    Medical Informatics:
    • Cohort discovery, EHR-based phenotyping, Predictive Modeling
    • Data quality assessment or validation
    • Decision support solutions
    • Interoperability (e.g., ontology, terminology, and others)
    • Machine learning for clinical applications
    • Mobile health and wearable devices

    PAPER SUBMISSION AND PUBLICATION

    Prospective authors are invited to submit unpublished work to ICIBM 2019. All submitted papers will be peer-reviewed. Acceptance to special issues will be based on review scores and topics. Publication will also depend on the final approval of editorial office and requires ICIBM registration. The accepted papers of registered authors will be published in special issues of several journals, including Genes, BMC Genomics, BMC Systems Biology, BMC Bioinformatics, BMC Medical Genomics, BMC Medical Informatics and Decision Making, and International Journal of Computational Biology and Drug Design (IJCBDD). Participants have two tracks for paper submissions:

    Track 1:
    All papers prepared for BMC Genomics, BMC Systems Biology, BMC Bioinformatics, BMC Medical Genomics, BMC Medical Informatics and Decision Making, and IJCBDD will be submitted through EasyChair Conference System easychair.org/conf[...]m2019. Please contact Dr. Xia Ning Xia.Ning[at]osumc.edu for any questions regarding the submission of track 1.

    Track 2:
    Papers can be directly submitted to the journal Genes. Reviews will be handled exclusively by the journal editors and will not be reviewed by the ICIBM 2019 review committee. Papers for special issue Genes should be directly submitted through sciforum.net/conf[...]M2019 and notify us upon your submission. Please contact Dr. Yan Guo YaGuo[at]salud.unm.edu for any questions regarding the submission of track 2.

    TRAVEL AWARDS

    The conference typically provides 20 travel awards to students/postdocs; awards will be granted through an NSF grant application.

    IMPORTANT DATES

    Deadline for paper submission: February 16, 2019
    Notification to authors of papers: March 23, 2019
    Deadline for abstract submission: March 30, 2019
    Notification to authors of abstracts: April 4, 2019
    Deadline for travel award application: May 1, 2019
    Conference early registration deadline: May 8, 2019
    Conference regular registration: May 9 – June 8, 2019
    ICIBM conference: June 9-11, 2019

    CONTACT

    icibm2019[at]easychair.org​

    Submitter

    March 21-22, 2019
    Florence, Italy
    conference.pixel-online.net/NPSE

    The objective of the Conference is to promote transnational cooperation and share good practice 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 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.

    IMPORTANT DATES

    Last Extended Deadline for submitting abstracts: January 14, 2019
    Notification of abstracts' acceptance / rejection: January 18, 2019
    Deadline for papers' submission: January 21, 2019
    Conference days: March 21-22, 2019

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

    All accepted papers will be included in the Conference Proceedings published by Filodiritto Editore with ISBN and ISSN codes. This publication will be sent to be reviewed for inclusion in Conference Proceedings Citation Index by Thomson Reuters (ISI-Clarivate). The publication will also be included in Academia.edu and indexed in Google Scholar.

    For further information, please contact us at the following address: science[at]pixel-online.net or visit the New Perspectives in Science Education conference website: conference.pixel-online.net/NPSE
    Resources: GPSRdocker: a docker-based container for bioinformatics
    Submitted by Gajendra P.S. Raghava; posted on Wednesday, December 19, 2018

    Submitter

    We are pleased to announce GPSRdocker, a docker-based container that provides genomics, proteomics and system biology resources. This will be useful for researchers and students working in the field of bioinformatics.

    I will highly appreciate your feedback on this container, which will help us to improve it further.

    AVAILABILITY

    See hub.docker.com/r/ra[...]cker/ or webs.iiitd.edu.in/gpsrdocker/
    Education: Assembly and Annotation of Genomes
    Submitted by Carlo Pecoraro; posted on Wednesday, December 19, 2018 (1 comment)

    Submitter

    February 11-15, 2019
    Berlin, Germany
    www.physalia-courses.org/cour[...]se20/

    Application deadline: January 10, 2019
    Instructor: Dr. Thomas Dan Otto (University of Glasgow, UK; www.physalia-courses.org/instructors/t28/)
    Assistant instructor: Mr. Maximilian Driller (Begendiv, Germany; bit.ly/2zcwmQT)

    OVERVIEW

    This course will introduce biologists and bioinformaticians to the concepts of de novo assembly and annotation. Different technologies, from Illumina, PacBio, Oxford Nanopoor and maybe 10X will be used mixed with different approaches like correction, HiC scaffolding to generate good draft assemblies. Particular attention will be given to the quality control of the assemblies and to the understanding how errors occur. Further, annotation tools using RNA-Seq data will be introduced. An outlook of potential analysis is given. In the end of the course the students should be able to understand what is needed to generate a good annotated genome.

    TARGETED AUDIENCE & ASSUMED BACKGROUND

    • Understand the concepts and quality of de novo assembly and annotation for genomes of all sizes, virus to mammals
    • Learn the advantages of the different sequencing technologies e.g. Illumina, Pacific Bioscience and Oxford Nanopore for de novo assembly and how to access the quality of genomes sequences
    • Hands on experience of common tools for de novo sequence assembly, including visualization, contig ordering, scaffolding and error correction
    • Hands on experience of gene finding, including the use of RNA-Seq data
    • Being comfortable to assemble and annotate genomes
    Session content: www.physalia-courses.org/cour[...]m-20/

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

    Here is the full list of our courses and Workshops: www.physalia-courses.org/courses-workshops/
    Surveys: Benchmark your pay in the 2019 Genomics Salary Survey
    Submitted by Eugene Mc Daid; posted on Monday, December 10, 2018

    Submitter

    The second annual Genomics Salary operated by Paramount and Front Line Genomics has been launched this week and is a unique survey that benchmarks the average salaries for roles within Genomics and Bioinformatics. The survey takes just 5 minutes to complete (and is completely confidential) and the overall survey findings will be published in January – giving you the chance to benchmark your earnings versus others in the industry.

    You will be able to access a detailed salary analysis across the industry, gaining valuable insights into various roles, levels of experience and specialisms. This information will no doubt prove valuable to anyone involved in Genomics whether you are seeking a new role or recruiting for your business.

    Take part in the survey here: www.pararecruit.com/abou[...]rvey/

    The 2018 survey had over 1,200 completers and identified some key topics including:
    • USA genomics salaries are double those in the UK
    • Sales & marketing is highest paid role within genomics
    • 26.8% gender pay gap in UK genomics
    • Brexit threat to UK genomics industry
    You can download a copy of last year's survey here: www.pararecruit.com/abou[...]rvey/

    By taking this survey you will receive a full copy of the results and also have the opportunity to enter into a prize draw with a chance of winning one of 3 prizes – £50 of Amazon vouchers, £100 Amazon voucher or a New iPad Mini 4.

    All responses will be kept confidential. Any identifying information will be kept in accordance with the Data Protection Act.

    Complete the survey directly on the survey monkey website here: www.surveymonkey.co.uk/r/Genomics19
    Submit Archive Subscribe

     

    Acknowledgments

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