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    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
    Education: Training in Bioinformatics for Beginners @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Tuesday, December 04, 2018

    January 15-18, 2019
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    faes.org/biotech82

    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 comprehensive set of bioinformatics concepts, tools and techniques, using a cloud based, 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 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.

    HIGHLIGHTS

    • Participants will use a Graphic User Interface based Linux Desktop environment, specially configured for bioinformatics analysis in the Amazon Cloud.
    • Training provided by experienced active NIH researchers
    • Cookbook style bound manual for all exercises
    • Direct, after training support through exclusive forum membership
    • Continuing Education Credits

    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

    Submitter

    June 27-28, 2019
    Florence, Italy
    conference.pixel-online.net/FOE/

    The objective of the Future of Education Conference is to promote transnational cooperation and share good practice in the field of education. The Future of Education conference is also an excellent opportunity for the presentation of previous and current education projects and initiatives. The Call for Papers is addressed to teachers, researchers and experts in the field of education as well as to coordinators of teaching and training projects.

    Experts in the field of education are therefore invited to submit an abstract of a paper to be presented in 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 (2384-9509) codes. This publication will be sent to be reviewed for inclusion in SCOPUS (www.elsevier.com/solutions/scopus) and Thomson Reuters. Papers will also be included in ACADEMIA.EDU (www.academia.edu) and Google Scholar.

    IMPORTANT DATES

    Deadline for submitting Abstracts: March 4, 2019
    Notification of Acceptance / Rejection for Abstracts: March 18, 2019
    Deadline for final submission of Papers: May 2, 2019
    Conference days: June 27-28, 2019

    For further information, please contact us at the following address: foe[at]pixel-online.net or visit the Future of Education conference website.

    Submitter

    December 10-14, 2018
    IIIT-Delhi campus, Delhi, India
    www.iiitd.ac.in/webstory/nwcbh

    Introduction: There is an exponential growth in the field of computational biology in last two decades; that includes mining of big genomic data. Aim of this workshop is to bring all the experts and participants working on wide range of problems on a single platform to understand progress and challenges in the field of computational biology. In this workshop, our focus will be on application of informatics/computers in the field of biology, medicine, drug discover and healthcare. Thus, participants working in the field of applied computation/informatics, industry, teaching or experimental science will be highly benefitted.

    Who should attend: All students, faculty, researchers & Industry professionals who are working or are interested in Computational Biology, Biomedicine, Health informatics and allied areas should attend this workshop.

    Please visit the website for more information.

    Sunday, November 11, 2018, 9 a.m.-5:30 p.m.
    Dallas, Texas, USA
    Held in conjunction with SC18 (sc18.supercomputing.org)
    Room D173, Lower Lobby D
    works.cs.cardiff.ac.uk

    The program of the 13th Workflows in Support of Large-Scale Science (WORKS) Workshop is now available (works.cs.cardiff.ac.uk/program.php).

    9:00-9:10 Welcome. Sandra Gesing and Rafael Ferreira da Silva
    9:10-10:00 Ilkay Altintas (invited keynote talk)
    10:00-10:30 Coffee Break

    Session "Scheduling and Resource Allocation":
    10:30-10:55 Reduction of Workflow Resource Consumption Using a Density-based Clustering Model. Qimin Zhang, Nathaniel Kremer-Herman, Benjamin Tovar, Douglas Thain
    10:55-11:20 Flux: Overcoming Scheduling Challenges for Exascale Workflows. Dong H. Ahn, Ned Bass, Albert ChuJim Garlick, Mark Grondona, Stephen Herbein, Joseph Koning, Tapasya Patki, Thomas R. W. Scogland, Becky Springmeyer, Michela Taufer
    11:20-11:45 LOS: Level Order Sampling for Task Graph Scheduling on Heterogeneous Resources. Carl Witt, Sam Wheating, Ulf Leser
    11:45-11:55 Energy-Aware Workflow Scheduling and Optimization in Clouds using Bat Algorithm. Yi Gu, Chandu Budati

    Session "Provenance and Enhanced Monitoring":
    11:55-12:20 A Practical Roadmap for Provenance Capture and Data Analysis in Spark-based Scientific Workflows. Thaylon Guedes, Vitor Silva, Marta Mattoso, Marcos Bedo, Daniel Oliveira
    12:20-12:30 End-to-End Online Performance Data Capture and Analysis for Scientific Workflows. George Papadimitriou, Cong Wang, Karan Vahi, Rafael Ferreira da Silva, Anirban Mandal, Zhengchun Liu, Rajiv Mayani, Mats Rynge, Mariam Kiran, Vickie E. Lynch, Rajkumar Kettimuthu, Ewa Deelman, Jeffrey S. Vetter, Ian T. Foster
    12:30-14:00 Lunch

    Session "Heterogeneous Architectures":
    14:00-14:25 Planner: Cost-efficient Execution Plans Placement for Uniform Stream Analytics on Edge and Cloud. Laurent Prosperi, Alexandru Costan, Pedro Silva, Gabriel Antoniu
    14:25-14:50 Dynamic Distributed Orchestration of Node-RED IOT Workflows Using a Vector Symbolic Architecture. Christopher Simpkin, Ian J. Taylor, Daniel Harborne, Graham Bent, Alun Preece, Raghu K. Ganti
    14:50-15:00 Optimizing the Throughput of Storm-based Stream Processing in Clouds. Huiyan Cao, Chase Q. Wu, Liang Bao, Aiqin Hou
    15:00-15:30 Coffee Break

    Session "Workflow Tools and Support Environment":
    15:30-15:55 DagOn*: Executing direct acyclic graphs as parallel jobs on anything. Raffaele Montella, Diana Di Luccio, Sokol Kosta
    15:55-16:20 WRENCH: A Framework for Simulating Workflow Management Systems. Henri Casanova, Suraj Pandey, James Oeth, Ryan Tanaka, Frédéric Suter, Rafael Ferreira da Silva
    16:20-17:30 Panel "The Future of Scientific Workflows: Challenges and Opportunities" (panelists will be announced soon)

    Submitter

    EXCERPT

    The selection of a first-line chemotherapy drug to treat many types of cancer is often a clear-cut decision governed by standard-of-care protocols, but what drug should be used next if the first one fails?

    That's where Georgia Institute of Technology researchers believe their new open source decision support tool could come in. Using machine learning to analyze RNA expression tied to information about patient outcomes with specific drugs, the open source tool could help clinicians chose the chemotherapy drug most likely to attack the disease in individual patients.
    Source: medicalxpress.com/news[...].html
    Education: Course on Snakemake workflow management system
    Submitted by Carlo Pecoraro; posted on Wednesday, November 07, 2018

    February 19-20, 2019
    Berlin, Germany
    www.physalia-courses.org/cour[...]se41/

    Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. is a workflow management system, consisting of a text-based workflow specification language and a scalable execution environment, that allows the parallelized execution of workflows on workstations, compute servers and clusters without modification of the workflow definition. Thereby, its scheduling algorithm allows Snakemake to maximize workflow execution speed while not exceeding given constraints like the number of available processor cores, cluster nodes or auxilliary hardware like graphics cards.

    Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about 5000 homepage visits per month, it has a large and stable user community.

    This course will introduce the Snakemake workflow definition language and describe how to use the execution environment to scale workflows to compute servers and clusters while adapting to hardware specific constraints. Further, it will be shown how Snakemake helps to create reproducible analyses that can be adapted to new data with little effort.

    Register now for the first 2-day Snakemake Workshop in Berlin with Johannes Köster johanneskoester.bitbucket.io

    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) and Thomson Reuters. Papers will also be included in Academia.Edu (www.academia.edu) and Google Scholar.

    IMPORTANT DATES

    Extended Deadline for submitting abstracts: Nov. 13, 2018
    Notification of abstracts' acceptance / rejection: Nov. 17, 2018
    Deadline for final submission of papers: Jan. 21, 2019
    Dates of the conference: Mar. 21-22, 2019

    FOR MORE INFORMATION

    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.
    Education: Training in Variant Analysis @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Monday, October 22, 2018

    November 13-16, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    faes.org/biotech79

    BACKGROUND

    Next generation sequencing technologies have made genotyping a day to day research and diagnostic tool. Genotyping has come all the way from bench-to-bedside. Genetic variants are being used in personalized medicine to identify susceptibility genes, common disease variants and mutations relevant for diagnosis and therapy.

    OBJECTIVES

    Participants will use popular open source tools and techniques necessary for analysing variants starting from raw data quality control. Apart from the regular analysis like alignment, variant calling and annotation, this training will walk through participants in several advanced variant analysis methods and techniques.

    Skill sets taught:
    • NGS Basics, experimental design, data format
    • Data quality control, preprocessing and alignment
    • Germline variant calling
    • Somatic variant calling
    • Variant score recalibration and filtering
    • Variant calling best practices
    • Indels, structural and copy-number variation
    • Cohort and population scale analysis
    • Recombination, linkage, LOH, haplotype, allelic imbalance
    • Variant annotation and association analysis
    • Co-variation, causal variation, network analysis
    Highlights:
    • Cloud-based Linux desktop
    • Training provided by active NIH researchers
    • Cookbook style bound manual for all exercises
    • Direct, after training support through exclusive forum membership
    • Continuing Education Credits
    Education: Free Webinar: Biomedical Data, Simplified
    Submitted by Sahil Sethi; posted on Friday, October 19, 2018

    Submitter

    Our recent webinar on the critical role data science tools and skills play in the advancement of biomedical research and precision medicine.

    Watch now: youtu.be/2Eyb-P1o_ls

    Announcing the start of an online training program designed to empower researchers, clinicians and students to handle their own high-throughput datasets and extracting insights through processing, analysis, machine learning and visualization. Learn more: edu.t-bio.info
    Submit Archive Subscribe

     

    Acknowledgments

    We wish to thank the following for their support:

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