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    September 11-14, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    faes.org/node[...]p;d4=

    OBJECTIVES

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

    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: Linux, R, Perl, Python
    • Platforms: EMBOSS, UGENE, H2O, Galaxy

    Sunday, September 9, 2018
    Athens, Greece (during ECCB2018)
    cpw2018.org

    Submission deadline for abstracts has been extended until August 15. Travel awards available!

    Digital and computational pathology are increasingly used to study biological processes and diseases as novel molecular probing and imaging techniques allow the measurement of single molecules in whole tissue sections. Resulting multi-gigapixel images can be viewed on a computer screen via dedicated software. However, automated analysis of such large-scale datasets is challenging and their combination with omics data is not trivial. This workshop wants to facilitate bridging opportunities between the bioinformatics and tissue image analysis communities.

    This second edition is organized as a full-day workshop during ECCB 2018 (www.eccb18.org).

    SCOPE

    Computational pathology exists at the interphase between bioinformatics, machine learning, and digital pathology (microscopy). Submissions from all topics of interest are welcome (non-exhaustive list):

    Machine learning and image analysis for quantification in digital pathology (in 2D & 3D), Novel approaches (e.g. spatial or graph-based methods) to extract high-level features (e.g. molecular networks or spatial expression patterns) from tissue images for systems pathology, Software development methodologies and tools to ease the exploitation of large tissue images and integration with omics data, Novel molecular imaging techniques on tissues (molecular pathology, next generation pathology) and their analysis challenges, e.g. in situ hybridization, mass spectrometry imaging of formalin-fixed paraffin-embedded tissues, mass cytometry, and other spectroscopy techniques (Raman, ...), ... Research applications on non-human model organisms

    KEYNOTE SPEAKERS

    The following keynote speakers are confirmed to speak at the conference:

    Thomas Fuchs, Memorial Sloan Kettering Cancer Center
    Chakra Chennubhotla, University of Pittsburgh
    Derek Magee, University of Leeds

    SUBMISSIONS

    The conference solicits oral talks, posters, and proceeding papers contributions of original work or work that was recently accepted or published in a peer-reviewed journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review.

    Conference proceedings will be published by the Journal of Pathology Informatics.

    The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session. For submission instructions, please refer to www.fourwav.es/cpw2018

    KEY DATES

    Submission deadline: August 15, 2018.
    Conference: Sunday September 9, 2018.

    Submitter

    June 28th, 2018, 4:00 pm to 7:00 pm (Eastern European Time)
    edu.t-bio.info/turkey-webinar/

    This RNA-seq workshop is perfect for those interested to get more hands-on practice with bioinformatics or to kick-start a project that has been sitting on the shelf, waiting for the right time. In the workshop, participants will have the opportunity to review and start using the T-BioInfo Bioinformatics platform (t-bio.info).

    The platform has dedicated sections to analyze Exome-Seq, RNA-Seq, Metagenomics and other "omics" data types. With a visual and intuitive interface that eliminates the need for coding, any clinician or biologist can prepare complex processing pipelines and deploy powerful machine learning algorithms to extract meaningful insights from large datasets. The approaches tested on this platform can be deployed independently and extended in a familiar environment like Excel or R for post-processing. Here is an example of the T-BioInfo platform in action:

    The workshop will address the basics of using the platform for RNA-seq data processing and downstream analysis. We will review bioinformatics concepts relevant to high-throughput data like data processing, exploration, analysis and interpretation. We will primarily focus on RNA seq data like gene/isoform expression, but the same concepts can apply to other types of data.

    After a demonstration of the T-BioInfo platform interface and review of methods in the supervised and unsupervised data mining sections, we will discuss free educational resources and our ongoing or planned pilots where students can gain practical experience and get involved in research opportunities. The platform is in public beta and has a research or educational account types available.

    August 7-10, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    faes.org/node[...]p;d=4

    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.

    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

    March 21-22, 2019
    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 conference.

    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 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.

    The New Perspectives in Science Education conference focuses on the following topics:
    • Biomedical Science Education
    • Chemistry Teaching Methods
    • Educational Strategies
    • Enhancing Students' Motivation
    • Health Education
    • Robotics Education
    • Science and Environment
    • Science and Nature
    • Science and Society
    • Science Education - Extra Curricula Activities
    • Science Education and Special Needs
    • Science Teachers Professional Development
    • Science Teaching in Primary and Middle School
    • Science Teaching Methods
    • STEM Education
    • Studies on Science Education
    • Training of Science Teachers

    IMPORTANT DATES

    Deadline for submitting abstracts: October 23, 2018
    Notification of Acceptance / Rejection: November 6, 2018
    Deadline for final submission of papers: January 21, 2019
    Dates of the conference: March 21-22, 2019

    Submitter

    August 8, 2018
    Fremont, CA, USA
    www.eventbrite.com/e/ha[...]90590

    Keck Graduate Institute is hosting a workshop with Pine Biotech CEO, Elia Brodsky and Dr. Kasthuri Kannan, professor of pathology from NYU Langone Medical School to discuss Machine Learning for Biomedical Data – a workshop session about tools, practices and applications.

    The workshop is perfect for management seeking hands-on experience for big data analytics in life sciences.

    This hands-on workshop will cover:
    • Processing steps for high-throughput "big" datasets
    • Exploring high throughput data (RNA-seq)
    • Preparation of gene and isoform expression data for machine learning
    And more

    During the workshop, participants will use the online T-Bioinfo platform which combines public domain and proprietary methods for processing, analysis, and integration of all types of -omics datasets.

    KGI is collaborating with Pine Biotech to deliver this outstanding workshop.

    Pine Biotech is on a mission to simplify bioinformatics and enable scientific discovery through their powerful multi-omics analysis platform, T-BIOINFO. Their goal is to bring the exciting new capabilities of big omics data analysis and integration into the hands of biomedical researchers through a simple and intuitive interface, innovative algorithms, integration, and visualization. They believe that in the hands of an increasing number of people, their platform will enable discoveries that will enhance human health and well being.

    Submitter

    EXCERPT

    Far from just being the product of our parents, University of Adelaide scientists have shown that widespread transfer of genes between species has radically changed the genomes of today's mammals, and been an important driver of evolution.

    In the world's largest study of so-called "jumping genes", the researchers have traced two particular jumping genes across 759 species of plants, animals and fungi. These jumping genes are actually small pieces of DNA that can copy themselves throughout a genome and are known as transposable elements.

    They have found that cross-species transfers, even between plants and animals, have occurred frequently throughout evolution.
    Source: phys.org/news[...].html

    Article: doi.org/10.1[...]456-7
    Education: Course on the analysis of single cell RNA-seq data
    Submitted by Carlo Pecoraro; posted on Wednesday, July 11, 2018

    February 25 – March 1, 2019
    FU University in Berlin
    www.physalia-courses.org/cour[...]se18/

    OVERVIEW

    In recent years single-cell RNA-seq (scRNA-seq) has become widely used for transcriptome analysis in many areas of biology. In contrast to bulk RNA-seq, scRNA-seq provides quantitative measurements of the expression of every gene in a single cell. However, to analyze scRNA-seq data, novel methods are required and some of the underlying assumptions for the methods developed for bulk RNA-seq experiments are no longer valid. In this course we will cover all steps of the scRNA-seq processing, starting from the raw reads coming off the sequencer. The course includes common analysis strategies, using state-of-the-art methods and we also discuss the central biological questions that can be addressed using scRNA-seq.

    FORMAT

    The course will be delivered over the course of five days. Each day will include a lecture and laboratory component. The lecture will introduce the topics of discussion and the laboratory sessions will be focused on practical hands-on analysis of scRNA-seq data. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate a skill as well as applying these skills on your own to complete individual exercises. After and during each exercise, interpretation of results will be discussed as a group. Computing will be done using a combination of tools installed on the attendees laptop computer and web resources accessed via web browser.

    TARGETED AUDIENCE & ASSUMED BACKGROUND

    This course is aimed at researchers and technical workers who are or will be analyzing scRNA-seq data. The material is suitable both for experimentalists who want to learn more about data-analysis as well as computational biologists who want to learn about scRNASeq methods. Examples demonstrated in this course can be applied to any experimental protocol or biological system.

    REQUIREMENTS

    • Working knowledge of unix (managing files, running programs)
    • Programming experience in R (writing a function, basic I/O operations, variable types, using packages)
    • Bioconductor experience is a plus.
    • Familiarity with NGS data and its analyses (using alignment and quantification tools for bulk sequencing data)

    INSTRUCTORS

    Dr. Ayshwarya Subramanian (Harvard School of Public Health, Broad Institute, Dana-Farber Cancer Institute, US)
    Dr. Dana Silverbush (Harvard School of Public Health, Broad Institute, Dana-Farber Cancer Institute, US)
    Dr. Ehsan Habibi (Harvard School of Public Health, Broad Institute, Dana-Farber Cancer Institute, US)

    Submitter

    To encourage bioinformaticists in India who have had made outstanding contributions in the area of Bioinformatics and Functional Genomics, we have initiated the Bioclues Innovation, Research and Development (BIRD) awards in 2011.

    Nominations are invited for outstanding contributions in the area of Functional Genomics and Bioinformatics. This award is meant not just for academicians but also for scientists who have shown exemplary excellence in the field of Bioinformatics. While scientists who have been working for not-for-profit organizations will be given importance, the ones who are working for commercial organisations are no less exception if the research they have carried out has been widely honoured and if they have made longstanding contributions. The awardee would receive a plaque and a citation with certificate. The awardee would further be invited to join the core/rep team of Bioclues society.

    ​More at ​http://bioclues.org/bird-awards/​
    Education: Course on Comparative Genomics
    Submitted by Carlo Pecoraro; posted on Monday, July 09, 2018 (1 comment)

    October 1-5, 2018
    Berlin, Germany
    www.physalia-courses.org/cour[...]se34/

    We still have a few places available for our course on "Comparative Genomics", which will take place this October (1-5) in Berlin.

    This course will introduce biologists and bioinformaticians into the field of comparative genomics. Different techniques will be introduced to identify single nucleotide polymorphism (SNP) and structural variations (SVs) as well as the annotation of these variations and the assessment for their functional impact.

    Our instructors are:
    Dr. Fritz J. Sedlazeck (Assistant Professor at the Human Genome Sequencing Center at Baylor College of Medicine, USA).
    Prof. Ingo Ebersberger (Professor for Applied Bioinformatics, Goethe University Frankfurt, Germany)

    Should you have any questions, please feel free to write to: info[at]physalia-courses.org.
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