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    Events: Bioinformatics for Big Data Conference
    Submitted by James Prudhomme; posted on Friday, December 15, 2017

    February 12-14, 2018
    San Francisco, CA
    www.triconference.com/bioi[...]-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)

    Submitter

    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 www.iprotein.info 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.

    AVAILABILITY

    www.iprotein.info
    Events: Integrated Pharma Informatics Conference
    Submitted by James Prudhomme; posted on Thursday, December 14, 2017

    February 12-14, 2018
    San Francisco, CA
    www.triconference.com/inte[...]atics

    Clinical trials, imaging, sequencing, EMRs, and other sources continue to generate a myriad of data points, and pharma plays a key role in driving a new reality of data-driven precision medicine. Integrated informatics is necessary to integrate, analyze, and interpret data from these sources, but understanding this data is only one challenge that the pharmaceutical industry faces. This conference will discuss the challenges that pharma faces today, how informatics projects are addressing those challenges, and how they are setting the stage for future opportunities.

    Top Pharma to discuss:
    • Driving self-serve informatics
    • Applications of machine learning and artificial intelligence in drug discovery and development
    • Data integration, analysis, and storage in the cloud
    • Projects in deep learning and real-world evidence data curation
    • Informatics for target validation and indication expansion
    • Translational informatics for precision medicine
    Visit our website to view the agenda, speaker abstracts, and to register.

    Organized by: Cambridge Healthtech Institute (CHI)

    January 9-12, 2018
    National Institutes of Health
    9000 Rockville Pike
    Bethesda, MD, USA
    faes.org/biotech78

    OBJECTIVE

    Data integration is a big problem in biomedical research, especially in the era of NGS data, BigData, "omics", precision medicine etc. Network based approach is one of the interesting and efficient ways to integrate data. This hands-on training will introduce participants to network concepts, data preparation and integration methods, data analysis, exploration and visualization using Cytoscape and other open source tools. The training also includes a one day Bring-Your-Own-Data clinic.

    Hands-on Skills/Tools taught:
    • Data Cleaning and Preparation: Basic Unix
    • Data Cleaning and Preparation: OpenRefine
    • Network Generation: Cytoscape
    • Data Integration: Cytoscape
    • Enrichment analysis: Cytoscape
    • Pathway analysis: Cytoscape
    • Gene Prioritization: Cytoscape
    • Data Exploration: Cytoscape
    • Data Visualization: Cytoscape
    • Large Graph Analysis: Neo4J

    Submitter

    EXCERPT

    Almost 15 years after scientists first sequenced the human genome, making sense of the enormous amount of data that encodes human life remains a formidable challenge. But it is also precisely the sort of problem that machine learning excels at.

    On Monday, Google released a tool called DeepVariant that uses the latest AI techniques to build a more accurate picture of a person's genome from sequencing data.
    Source: www.technologyreview.com/s/60[...]nome/

    DeepVariant on GitHub: github.com/google/deepvariant

    Submitter

    EXCERPT

    A DNA testing kit might sound like a fun holiday gift to share with a loved one, but [US Senator] Chuck Schumer says it might be dangerous to give companies that market them access to your genetic codes.

    Schumer said it's unclear what companies like AncestryDNA do with all the data they collect from hair or saliva samples that clients – eager to know if they're 20 percent Cherokee or have a genetic marker for a certain disease – send in.
    Source: nypost.com/2017[...]info/

    Schumer's statement has led to a petition "demanding that Ancestry and 23andMe change their policies and withhold genetic information from law enforcement": www.thepetitionsite.com/278/[...]lice/

    Submitter

    March 22-23, 2018
    Florence, Italy
    conference.pixel-online.net/NPSE

    The objective of the New Perspectives in Science Education 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, 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 New Perspective in Science Education international conference. The abstract should be written in English and submitted no later than December 19, 2017 (extended deadline). In order to submit an abstract please visit our website: conference.pixel-online.net/NPSE[...]n.php.

    IMPORTANT DATES

    Extended Deadline for submitting abstracts: December 19, 2017
    Notification of Acceptance / Rejection for Abstracts (Deadline 22 November): December 13, 2017
    Notification of Acceptance / Rejection for Abstracts (Deadline 19 December): January 8, 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 (www.elsevier.com/solutions/scopus). Papers will also be included in ACADEMIA.EDU (www.academia.edu) and 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
    Education: Training in Computational Drug Design and Discovery at NIH
    Submitted by Vijayaraj Nagarajan; posted on Wednesday, November 08, 2017

    December 12-15, 2017
    National Institutes of Health
    9000 Rockville Pike
    Bethesda, MD, USA
    faes.org/biotech66

    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.

    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.

    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)

    December 18-20th, 2017
    Naples, Italy
    www.bbcc-meetings.it

    12th Edition

    The Call for Abstracts for Poster Presentations is still open.

    Deadline is fixed on November 4th.

    Program of oral presentations will be announced in the next week. Please visit the conference web site for information about it, confirmed invited speakers, post-proceedings publications and any other information.
    Events: Applied Bioinformatics in Life Sciences (2nd Edition)
    Submitted by Alexander Botzki; posted on Thursday, November 02, 2017

    March 8-9, 2018
    Leuven, Belgium
    vibconferences.be/even[...]ition

    CALL FOR ABSTRACTS

    As an integral part of biological research, the field of bioinformatics brings forth innovative computational approaches leading to high-impact results in an increasingly data-dense environment.

    After a sold-out first edition in March 2016, this second edition will feature recent developments in bioinformatics research, and highlight the power of computational biology in the fields of medical, agricultural, and biotechnology research. Renowned speakers will present how bioinformatics is applied broadly in life sciences, and shed light on the future perspectives of their research.

    ​Conference attendees will have ample networking opportunities besides an exciting scientific program.

    Abstract submission: vibconferences.be/user[...]D3618

    Find out more about the first edition 'ABLS' – vibconferences.be/even[...]ences

    CONFERENCE TRACKS

    • Medical Integrative Omics
    • Proteomics and Metabolomics
    • Structural Bioinformatics
    • Systems Biology

    IMPORTANT DATES

    Full Abstract Submission Deadline: January 18, 2018
    Early Bird Conference registration Deadline: January 25, 2018
    Final Conference registration Deadline: February 22, 2018

    For more information, please contact:
    VIB Conferences
    Phone: +32 9 244 66 11
    Email: conferences[at]vib.be
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