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    Submitter

    We are pleased to announce a new resource from our group for predicting cell penetration peptides containing modified residues, which may serve as drug delivery vehicles.

    AVAILABILITY

    Web server link: webs.iiitd.edu.in/raghava/cellppdmod/

    ARTICLE

    Paper link: www.frontiersin.org/arti[...]/full

    May 8-11, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]0f112

    BACKGROUND

    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.

    Hands-on Skills/Tools Taught:
    • Command line tools will be presented
    • Galaxy web based platform will be used to analyze primary data
    • Cloud computing
    • Genomic databases
    • De novo assembly will be surveyed

    April 24-27, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]16440

    BACKGROUND

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

    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.

    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

    June 10-12, 2018
    Los Angeles, CA, USA
    icibm2018.zhaobioinfo.org

    The purpose of the 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) 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.)
    Bioinformatics:
    • 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

    PAPER SUBMISSION

    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), Human Heredity, and Quantitative Biology. Authors need to prepare manuscripts in the format of the corresponding journal that they prefer.

    TRAVEL AWARDS

    Up to 20 travel awards for students and postdocs are open for applications: See here for details: icibm2018.zhaobioinfo.org/Travel.htm#award

    REGISTRATION

    Registration site: icibm2018.zhaobioinfo.org/Registration.htm

    IMPORTANT DATES

    Conference early registration opens: April 1, 2018
    Conference early registration deadline: May 10, 2018
    Deadline for travel award application: May 1, 2018
    Conference regular registration: May 11 - June 10, 2018
    ICIBM 2018 conference: June 10-12, 2018
    Education: Epigenomics Workshop in Berlin
    Submitted by Carlo Pecoraro; posted on Thursday, March 29, 2018

    May 28 - June 1, 2018
    Berlin, Germany
    www.physalia-courses.org/cour[...]se31/

    OVERVIEW

    This course will introduce researchers and technical workers to the bioinformatic analysis of large epigenomic data sets obtained using Next-Generation Sequencing (NGS) technologies, with a focus on ChIP-seq, RNA-seq and DNase-seq / ATAC-seq. The course will cover the theoretical foundations of the most widely adopted algorithms and analysis pipelines, a targeted introduction to scripting in bash and R/BioConductor, and extensive hands-on tutorials using publicly available NGS data sets. At the end of this course, the students should be able to efficiently analyze their own data and identify common pitfalls of genomics data analyses.

    INSTRUCTORS

    Dr. Federico Comoglio ( Division of Gene Regulation, Netherlands Cancer Institute)
    Dr. Iros Barozzi (Imperial College London (UK))

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

    Submitter

    Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens. Available genomic data for pathogens have created new opportunities for drug discovery and development to fight them, including new resistant and multiresistant strains. In particular structural data must be integrated with both, gene information and experimental results. In this sense, there is a lack of an online resource that allows genome wide-based data consolidation from diverse sources together with thorough bioinformatic analysis that allows easy filtering and scoring for fast target selection for drug discovery. Here, we present Target-Pathogen database (target.sbg.qb.fcen.uba.ar/patho), designed and developed as an online resource that allows the integration and weighting of protein information such as: function, metabolic role, off-targeting, structural properties including druggability, essentiality and omic experiments, to facilitate the identification and prioritization of candidate drug targets in pathogens. We include in the database 10 genomes of some of the most relevant microorganisms for human health (Mycobacterium tuberculosis, Mycobacterium leprae, Klebsiella pneumoniae, Plasmodium vivax, Toxoplasma gondii, Leishmania major, Wolbachia bancrofti, Trypanosoma brucei, Shigella dysenteriae and Schistosoma Smanosoni) and show its applicability. New genomes can be uploaded upon request.

    AVAILABILITY

    Please visit target.sbg.qb.fcen.uba.ar/patho

    ARTICLE

    Nucleic Acids Res. 2018 Jan 4;46(D1):D413-D418. doi.org/10.1093/nar/gkx1015.
    Opportunity: Invitation for geXc Boston 2018, Symposium
    Submitted by Bhavyasri Vennapusa; posted on Monday, March 26, 2018

    May 18th, 8:30 am - 6:30 pm
    Broad Institute, Cambridge, MA, USA
    www.gexcsymposia.com

    It is with excitement and great pleasure to announce geXc Boston 2018, an educational Genomics symposium, being held at the Broad Institute on May 18th.

    geXc Boston 2018 is a gathering of thought leaders from the Boston research community, to deliver powerful talks on the latest trends, applications and solutions in Genomics and Computational Genomics. This free symposium, which includes a poster competition and a social event, offers an amazing opportunity for speakers, researchers, graduate students, and industry to discuss their research interests, learn from cutting-edge colleagues, and network in their research community. As we announce this much awaited event, we invite all genomic enthusiasts to partake in this symposium and take advantage of this opportunity. Please feel free to share this information with your peers and research groups.

    About geXc:
    geXc, the 'Genomic Exchange Community' symposia series is a grassroots initiative with an intent to improve genomics through collaboration and innovation. As you know, genomics holds great promise for advancing our understanding of all living organisms. Technological advancements in genomics continue to come at alarming rate; there are numerous complexities to consider. For the uninitiated, planning for an initial experiment and coping with data, can be overwhelming. To help guide discovery and development in genomics, we assemble leading experts, both academic and industry, to share their work and experiences.

    Our goal:
    The objective of this symposium is to provide a forum for sharing, learning, and networking. The symposium is open to anyone who is interested in Genomics and Computational Genomics.

    geXc symposium:
    This full day event, including the revered social and student poster competition ($ prizes) is funded by our gracious sponsors and because of their contributions, the event is completely free for attendees. (breakfast, lunch, coffee, snacks, wine & cheese included).

    geXc statistics:
    The geXc symposia have been held for the past 6 years, covering over 275 Topics by 175 Speakers and have attracted over 4000 scientists.

    Call for posters:
    Calling all graduate students (or really anyone that would like to present a poster)! Your poster entry is welcome! The top three posters win cash prizes.

    Venue:
    The Broad Institute Auditorium, 415 Main Street, Cambridge, MA

    Please visit www.gexcsymposia.com for the list of speakers, sponsors and registration details.

    Please feel free to contact us at bhavya[at]d-markbio.com for any queries.
    Education: Training in Bioinformatics for Beginners @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Monday, March 19, 2018

    April 17-20, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]p;ch=

    BACKGROUND

    Bioinformatics (Computational Biology) is a must skill required in every modern biomedical research lab. Installing and configuring a wide variety of computational biology tools is a cumbersome task that requires software engineering skills. This hands-on training course will introduce participants to a custom, all-in-one, fully loaded linux desktop (with windows like graphical user interface) machine, that comes with hundreds of popular computational biology (bioinformatics) tools required for a successful modern biomedical research lab.

    OBJECTIVES

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

    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: R, Perl, Python
    • Platforms: EMBOSS, UGENE, H2O, Galaxy
    Awards: Announcing the 2018 Benjamin Franklin Award laureate
    Submitted by J.W. Bizzaro; posted on Thursday, March 15, 2018

    Submitter

    We are happy to announce that the members of Bioinformatics.org have chosen by vote Desmond Higgins of the University College Dublin (UCD) Conway Institute as the laureate of the 2018 Benjamin Franklin Award for Open Access in the Life Sciences!

    The Higgins lab has developed the CLUSTAL series of multiple sequence alignment tools, which are among the very first bioinformatics tools used by any student and are fundamental to the field, so it's very much an honor for us to recognize Des for his contribution.

    The ceremony will take place on May 17th at the Bio-IT World Conference & Expo (www.bio-itworldexpo.com) in Boston, Massachusetts. We hope to see you there!
    Education: FORCE11 Scholarly Communication Institute (FSCI)
    Submitted by Suzi Smith; posted on Monday, March 05, 2018

    July 30 - August 3, 2018
    University of California San Diego (UCSD), La Jolla, CA, USA
    www.force11.org/fsci/2018

    The FORCE11 Scholarly Communications Institute at the University of California, San Diego is a week long summer training course, incorporating intensive coursework, seminar participation, group activities, lectures and hands-on training. Participants will attend courses taught by world-wide leading experts in scholarly communications. Participants will also have the opportunity to discuss the latest trends and gain expertise in new technologies in research flow, new forms of publication, new standards and expectations, and new ways of measuring and demonstrating success that are transforming science and scholarship.
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