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  • News & Commentary - News

    Latest announcements
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    Submitter

    Repositive, the company that created the world's largest portal for accessing human genomic research data, has closed a Series A funding round of £2.5m.

    This investment will allow Repositive to expand its commercial offering through the development of premium features for it's fast growing community of platform users worldwide. Alongside this, Repositive will invest further in expanding the range of data sources on its platform and developing further commercial products and services for the genomics R&D industry. Repositive welcomes Ananda as lead investor and sees the continued support of Amadeus Capital Partners and Jonathan Milner.

    Read the Press Release: blog.repositive.io/pres[...]lion/

    How will investments grow community? blog.repositive.io/how-[...]nity/

    Browse Repositive's 1.1 million human genomic datasets: discover.repositive.io
    Events: CfP: RECOMB Comparative Genomics 2017
    Submitted by Joao Meidanis; posted on Monday, April 24, 2017

    October 4-6, 2017
    Centre for Genomic Regulation (CRG), Barcelona, Spain
    www.crg.eu/en/e[...]kshop

    SCOPE

    The annual RECOMB Comparative Genomics Satellite Conference (RECOMB-CG) brings together leading researchers in the mathematical, computational and life sciences to discuss cutting edge research in comparative genomics, with an emphasis on computational approaches and the analysis of novel experimental results. The program will include keynote talks, contributed talks, and a poster session.

    With this Call for Papers we invite high-quality original full papers on topics related to the conference theme. The conference will also have a poster session. A detailed call for posters will be published later on the conference web page.

    TOPICS

    Papers are solicited on, but not limited to, the following topics: genome evolution; genome rearrangements; genome variation, diversity and dynamics; phylogenomics; comparative tools for genome assembly; population genomics; comparison of functional networks; comparative epigenomics; paleogenomics; cancer evolution genomics; epidemiology; gene identification and/or annotation.

    IMPORTANT DATES

    Paper Submission Deadline: June 11, 2017
    Author Notification: July 7, 2017
    Final Version Due: July 21, 2017
    Conference: October 4-6, 2017

    FOR MORE INFORMATION

    Contact: meidanis[at]ic.unicamp.br, nakhleh[at]rice.edu

    Submitter

    EXCERPT

    The analysis, presented last month at the Annual Clinical Genetics Meeting in Phoenix, showed that whole-genome sequencing can sometimes provide a diagnosis when previous whole-exome sequencing couldn't. But it also reveals that the genome is still not well understood and that scientists don't yet know all the alterations in the genome that may cause disease.

    Isaac Kohane, of Harvard Medical School's Department of Biomedical Informatics, says people analyzing a genome might simply miss a cause lying in plain sight – a so-called false negative.

    "Our ability to distinguish what actually might cause disease is still quite crude," Kohane says. "So we have an unknown false-negative rate."
    Source: www.technologyreview.com/s/60[...]osis/
    Events: Proving the Potential: Health Data Standards Code-a-Thon
    Submitted by Cait Ryan; posted on Wednesday, April 19, 2017

    Last week the Office of the National Coordinator for Health Information Technology (ONC) announced a health standards and data innovation Code-a-Thon that requires contestants to develop projects that leverage one or more open tools and services created for the Patient Matching Aggregation and Linkage project. In less than 24 hours, submissions will be developed and presented to a panel of judges that uncover underlying gaps and support one of the following obstacles in Health IT:
    1. Electronic Quality Measures and/or decision support
    2. Secure and privacy preserving methods to aggregate patient data
    3. Discovery of patients, providers, researchers and/or services
    Up to $15,000 in prizes will be awarded to as many as 12 teams. Award amounts are as follows:

    First Prize: $5,000
    Second Prize: $2,000 each
    Third Prize: $1,000 each
    Honorable mentions: $500 each

    Winner announcements will be made at the close of the event, April 25th from 12-12:30pm.

    For detailed information about the Code-a-Thon, eligibility and submission requirements, and evaluation criteria, and to register, please visit the Code-a-Thon website: www.cccinnovationcenter.com/chal[...]thon/
    Events: Bioinformatics and Translational Research (BioTransR 2017)
    Submitted by paul; posted on Wednesday, April 12, 2017

    May 15-16, 2017
    Hesperia Tower Hotel, Barcelona, Spain
    www.etriks.org/bioi[...]2017/

    Making sense of today's translational research data requires a team approach. The datasets that are generated today are complex, and involve many different types of data. The consequence is that the integration of multiple types expertise is necessary. In this meeting, data scientists and translational researchers will work together to build a common understanding of today's research data challenges. The aim is to find ways to help fulfill the promise of better health through the optimal use of data.

    This meeting is being organised by IMI funded project eTRIKS, which over the course of 4 years has helped over 50 translational research projects to get more value out of their data. It has become apparent over the course of those 4 years that the awareness about data infrastructure that is available for translational research is lacking. Thus, the 2 main themes of the meeting are: understanding the landscape of bioinformatics infrastructure and how to reduce fragmentation, and giving translational researchers the knowledge and the tools they need to collaborate on making sense of translational research data faster.

    Check out our meeting program: www.biosciconsulting.com/wp-c[...]e.pdf

    We have training (also live webinar) on CDISC standards, data curation, translational researcher training on tranSMART and programmer sessions. All free of charge.

    Register for free via www.etriks.org/bioi[...]2017/ – only few spots left!!

    If you wish to stay at Hesperia Tower Hotel, you can book a room directly at www.nh-hotels.com/even[...]-2017

    Submitter

    What's New in version 2:
    • Install module for Linux and MAC users → this module will auto install all the required dependencies for running RNA-SEQ pipelines using CSBB
    • Ability to process RNA-SEQ data (Single and Paired End)
    • Ability to generate TPM and Counts matrices for both Isoforms and Genes
    • Updates to existing Modules
    • RNA-SEQ pipelines workflow for human (hg19) and mouse (mm10)
    • RNA-SEQ pipelines for other genomes can be added on request from users
    • Auto download and update for R packages
    • Bug Fixes
    (Version2 addition/updates only for MacOS and LINUX; RNA-SEQ pipeline does not work for Windows currently.)

    MODULES

    Install: This module helps in auto installing all the required dependencies for running RNA-SEQ modules through CSBB. This module installs samtools, bowtie2, RSEM, bedtools, wget and fastqc. Install module run is required as a one-time process before attempting RNA-SEQ process modules of CSBB.

    UpperQuantile: Upper quantile normalization is used to normalize two or more distributions in absence of a reference distribution. Given a matrix of size M x N, where M is the number of rows and N is the number of columns, UpperQuantile will determine the 75th quantile value for ith column and normalize it across ith column. Upper quantile normalization is regularly used to remove variation from global gene expression data from microarrays and next generation sequencing data.

    BasicStats: This module is designed for some basic and quick statistical calculations on gene expression data across samples. BasicStats calculates mean, median, median adjusted deviation, standard deviation, variance, minimum and maximum for each gene based on expression across samples. Assume, you have m*n matrix where m are rows (genes) and n are columns (samples). BasicStats will calculated above mentioned statistics for each row (gene).

    ExpressionToZscore: This module converts expression values to z-scores. This module is helpful when a user wants to compare expression data from different sources (labs or platforms). This module converts expression value of a gene in each sample to z-score based on expression across the samples. Let's say there is a m*n expression matrix then each value in the matrix will be converted to z-score based on values for each row across columns.

    ExtractGeneInfo: This module helps to extract information/expression for a list of genes from a large matrix of genes and their expression/information across samples/columns. Let's say you have mn matrix and a list of 'a' items where a

    AVAILABILITY

    Download CSBB-v2.0 for free! Computational Suite for Bioinformaticians and Biologists sourceforge.net/projects/csbb-v2-0/
    Awards: Announcing the 2017 Benjamin Franklin Award laureate
    Submitted by J.W. Bizzaro; posted on Tuesday, April 04, 2017

    Submitter

    We are happy to announce that the members of Bioinformatics.org have chosen Rafael Irizarry of Harvard University and the Dana Farber Cancer Institute as the laureate of the 2017 Benjamin Franklin Award in the Life Sciences!

    The ceremony for the presentation of the award will be held at the 2017 Bio-IT World Conference & Expo in Boston (www.bio-itworldexpo.com). It involves a short introduction, the presentation of the certificate, and the laureate seminar.

    In the words of his nominators, Rafael has dedicated his career to developing methods and open source software for helping researchers genomics data. As a biostatistician, he has made fundamental advances in the science of analyzing large, noisy and biased genomics datasets. His contributions are particularly crucial in an era where archives are filling with tens of thousands of large open datasets; to re-use and combine these in any effective way requires a careful approach that considers technical confounders, batch effects, and other issues. See e.g. his work on Frozen robust multiarray analysis (fRMA) (www.ncbi.nlm.nih.gov/pubmed/20097884) & The Gene Expression Barcode (barcode.luhs.org).

    Rafael is also a contributor to and a leader of the influential Bioconductor project (www.bioconductor.org), which has helped to popularize open source software and open software development in the genomics and statistical communities. Examples of software packages that he's developed with his trainees and collaborators include affy, gcrma, oligo, minfi, and bumphunter, all of which are among the top 75 most downloaded Bioconductor packages. Several of Rafael's trainees have also made substantial methods and open-source software contributions, including through Bioconductor.

    He is also an accomplished educator. Rafael has authored and openly released excellent teaching materials. He developed and instructs the popular R and Statistics for the Life Sciences online course at HarvardX (online-learning.harvard.edu/cour[...]d-r-0), enrolling over 30,000 students a year. This course is part of the HarvardX Biomedical Data Science Open Online Training Curriculum developed by Rafael. The text book used in this course can be downloaded for free, and the R markdown code used to create the book is available on GitHub (genomicsclass.github.io/book[...].html).

    More about Rafael: rafalab.github.io
    Events: Rocky Mountain Bioinformatics Conference
    Submitted by Suzi Smith; posted on Wednesday, March 22, 2017

    December 7-9, 2017
    The Westin Hotel
    100Elbert Lane
    Snowmass Village, CO 81615
    www.iscb.org/rocky2017

    The Rocky series began fourteen years ago as a regional conference, and has grown into an international program with a spotlight on regional development in the computational biosciences. The presenters of the Rocky conference are scientists representing a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries from around the world. The meeting is a chance to get to know your colleagues near and far, seek collaborative opportunities, and find synergies that can drive our field forward.

    FOR MORE INFORMATION

    Contact:
    Stephanie Hagstrom
    admin[at]iscb.org

    Submitter

    October 16-18, 2017
    Palermo, Italy
    http://www[...]2017/

    CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS AND POSTERS

    The Workshop "Methods, tools & platforms for Personalized Medicine in the Big Data Era" is organised by NETTAB (International Workshop Series on Network Tools and Applications for Biology), and it will be held at the local research area of italian CNR (National Research Council) in Palermo.

    Confirmed Speakers:
    • Winston Hide, Professor of Computational Biology, University of Sheffield, UK.
    • Anita Grigoriadis, Lecturer in Cancer Bioinformatics, King's College, London, UK.
    Further Keynote speakers will be announced soon.

    TOPICS

    The topics of the joint event include, beside the usual NETTAB workshops topics, an additional special event topic.

    Methods, tools & platforms for Personalized Medicine in the Big Data Era (Special Event Topic), including:
    • Data management: Biomedical Big Data Management, Standards for Clinical and Genetic Data, Data Privacy and Security, Omics Data Integration, Biobanks
    • Data analysis: Omics Data analysis, Genetic Mutation Analysis, Biomarkers Discovery, NGS Data Analysis, Patient Information Analytics
    • Tools and Services: Clinical Genomics Services, Models for Clinic and Genetic Data, Mobile tools and applications, Interoperability of Clinical and omic tools, Communication Technologies for Health-Care.
    • Platforms: Integrated Data Warehouses, Integration of Applications and Data Services, Clinical Decision Support Systems, Healthcare Systems
    NETTAB Workshop topics:
    Bioinformatics methods, standards, tools, applications and experiences deployed over Internet, including:
    • On-line databases, software tools, user interfaces
    • Data integration and data fusion platforms, integrated bio-search
    • Grid and clouds applications and platforms
    • APIs and Web Services, workflow management platforms
    • Semantic tools, biomedical ontologies
    • Semantic Web tools, Linked Open Data, SPARQL endpoints
    • Biological Wikis, social applications for life sciences
    • Tools for collaborative development of software, databases and documents
    • Mobile bioinformatics apps

    IMPORTANT DATES

    Submission deadlines:
    Abstracts for oral communications: May 26, 2017
    Abstracts for posters: TBA
    Abstracts for software demo: TBA
    Abstracts for late posters: TBA
    A post workshop Supplement publication is planned, see below.

    INSTRUCTIONS FOR AUTHORS

    Submissions are welcome for oral communications, for posters and for software demos.
    All abstracts must be submitted as PDF files through EasyChair at www.easychair.org/conf[...]b2017
    The maximum length is 4 pages for oral communication abstracts and 2 pages for poster abstracts.
    Full instructions for authors are available at www.igst.it/nett[...]hors/

    PUBLICATION IN THE BOOK OF ABSTRACTS

    Accepted abstracts, both for oral communications and for posters, will be considered for the publication in the proceedings of the event, which will consist in a Collection in PeerJ Preprints.
    No Copyright form or permission is required for the publication of abstracts, since the proceedings wonÕt be an official publication.

    POST-WORKSHOP PUBLICATION

    A post workshop Special Issue in an International Journal with IF will be published with best full papers from presentations, both oral and poster, given at the Workshop. A special Call for papers will be launched shortly after the workshop (planned time presently is early November 2017). A publication fee could be requested for publication of accepted papers because of Open Access policies adopted by many journals.

    VENUE

    The Workshop and all satellite events will be held at the local research area of the Italian National Research Council, via Ugo La Malfa 153, 90146, Palermo.

    CHAIRS

    Paolo Romano & Alfonso Urso & Alfonso Valencia (Workshop Chairs)

    CONTACTS

    Email: nettab.workshops[at]gmail.com
    Twitter: @NETTABWorkshops
    LinkedIn: www.linkedin.com/grou[...]ofile
    Announce mailing list: groups.google.com/foru[...]ounce

    Submitter

    November 7-9, 2017
    Jaipur, India
    www.inbix.bioclues.org

    We have a great line-up of speakers, with Profs. Temple Smith and Thomas Ponten giving the keynotes, and talks by well known bioinformatics leaders in India. We encourage your submissions in the form of video abstracts, poster stub talks, elevator pitches, ideation/coding challenges, oral presentations, etc.

    Jaipur is a joyous city, and we welcome you for the exciting season in November.

    Please watch for the early bird registration deadline. Discounts are available for ISCB/Bioclues members, with an additional group discount applicable.

    We look forward to seeing you in "Joy"pur!
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