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    There was a recent blog post from Semantic Scholar - a competitor to Google Scholar - where they found the most-mentioned GitHub repos in the biomedical literature. They extracted the URLs for the repos from the body text of the papers. The blog post is at[...]1930a

    Full disclosure: I work on the Semantic Scholar project and was the one who wrote the blog post. It's pretty cool because we looked at the top repos mentioned by any biomedical paper in our corpus, but it turned out that almost everything was bioinformatics rather than other areas of biology.


    June 9-11, 2019
    Columbus, Ohio, USA

    It is our great pleasure to announce the 7th International Conference on Intelligent Biology and Medicine (ICIBM 2019). ICIBM is a high caliber conference which brings 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. The purpose of the ICIBM is to provide a congenial atmosphere highly conducive to extensive discussion and networking.


    You are invited to submit papers with unpublished original work describing recent advances on all aspects of Bioinformatics, Intelligent Computing, Systems Biology, and Medical Informatics, including but not restricted to the following topics:

    • Genomics and genetics, including integrative & functional genomics, genome evolution
    • Next generation sequencing data analysis, applications, and software and tools
    • Big data science including storage, analysis, modeling, visualization, and cloud
    • Precision medicine, translational bioinformatics and medical informatics
    • Drug discovery, design, and re-purposing
    • Proteomics, and protein structure prediction, molecular simulation and evolution
    • Single cell sequencing data analysis
    • Microbiome and Metagenomic
    Intelligent Computing:
    • Artificial intelligence, machine learning, deep learning, data mining, knowledge discovery
    • Natural language processing, literature mining, semantic ontology, and health informatics
    • Neural computing, kernel methods, feature selection/extraction
    • Evolutionary computing, swarm intelligence / optimization, ensemble methods
    • Manifold learning theory, artificial life and artificial immune
    • Image analysis and processing
    Systems Biology:
    • Modeling and simulation of biological processes, pathways, and networks
    • Mathematical and quantitative models of cellular and multi-cellular systems
    • Multi-dimensional omics data integration
    • Synthetic biological systems
    • Metabolomics, microbiome, and lipidomics
    • Self-organization in living systems (cells, organisms, swarms, ecosystems, etc.)
    • Applications of systems biology approaches to biomedical studies
    Medical Informatics:
    • Cohort discovery, EHR-based phenotyping, Predictive Modeling
    • Data quality assessment or validation
    • Decision support solutions
    • Interoperability (e.g., ontology, terminology, and others)
    • Machine learning for clinical applications
    • Mobile health and wearable devices


    Prospective authors are invited to submit unpublished work to ICIBM 2019. All submitted papers will be peer-reviewed. Acceptance to special issues will be based on review scores and topics. Publication will also depend on the final approval of editorial office and requires ICIBM registration. The accepted papers of registered authors will be published in special issues of several journals, including Genes, BMC Genomics, BMC Systems Biology, BMC Bioinformatics, BMC Medical Genomics, BMC Medical Informatics and Decision Making, and International Journal of Computational Biology and Drug Design (IJCBDD). Participants have two tracks for paper submissions:

    Track 1:
    All papers prepared for BMC Genomics, BMC Systems Biology, BMC Bioinformatics, BMC Medical Genomics, BMC Medical Informatics and Decision Making, and IJCBDD will be submitted through EasyChair Conference System[...]m2019. Please contact Dr. Xia Ning Xia.Ning[at] for any questions regarding the submission of track 1.

    Track 2:
    Papers can be directly submitted to the journal Genes. Reviews will be handled exclusively by the journal editors and will not be reviewed by the ICIBM 2019 review committee. Papers for special issue Genes should be directly submitted through[...]M2019 and notify us upon your submission. Please contact Dr. Yan Guo YaGuo[at] for any questions regarding the submission of track 2.


    The conference typically provides 20 travel awards to students/postdocs; awards will be granted through an NSF grant application.


    Deadline for paper submission: February 16, 2019
    Notification to authors of papers: March 23, 2019
    Deadline for abstract submission: March 30, 2019
    Notification to authors of abstracts: April 4, 2019
    Deadline for travel award application: May 1, 2019
    Conference early registration deadline: May 8, 2019
    Conference regular registration: May 9 – June 8, 2019
    ICIBM conference: June 9-11, 2019




    March 21-22, 2019
    Florence, Italy

    The objective of the 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 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.


    Last Extended Deadline for submitting abstracts: January 14, 2019
    Notification of abstracts' acceptance / rejection: January 18, 2019
    Deadline for papers' submission: January 21, 2019
    Conference days: March 21-22, 2019

    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 Conference Proceedings Citation Index by Thomson Reuters (ISI-Clarivate). The publication will also be included in and indexed in Google Scholar.

    For further information, please contact us at the following address: science[at] or visit the New Perspectives in Science Education conference website:
    Resources: GPSRdocker: a docker-based container for bioinformatics
    Submitted by Gajendra P.S. Raghava; posted on Wednesday, December 19, 2018


    We are pleased to announce GPSRdocker, a docker-based container that provides genomics, proteomics and system biology resources. This will be useful for researchers and students working in the field of bioinformatics.

    I will highly appreciate your feedback on this container, which will help us to improve it further.


    See[...]cker/ or
    Education: Assembly and Annotation of Genomes
    Submitted by Carlo Pecoraro; posted on Wednesday, December 19, 2018 (1 comment)


    February 11-15, 2019
    Berlin, Germany[...]se20/

    Application deadline: January 10, 2019
    Instructor: Dr. Thomas Dan Otto (University of Glasgow, UK;
    Assistant instructor: Mr. Maximilian Driller (Begendiv, Germany;


    This course will introduce biologists and bioinformaticians to the concepts of de novo assembly and annotation. Different technologies, from Illumina, PacBio, Oxford Nanopoor and maybe 10X will be used mixed with different approaches like correction, HiC scaffolding to generate good draft assemblies. Particular attention will be given to the quality control of the assemblies and to the understanding how errors occur. Further, annotation tools using RNA-Seq data will be introduced. An outlook of potential analysis is given. In the end of the course the students should be able to understand what is needed to generate a good annotated genome.


    • Understand the concepts and quality of de novo assembly and annotation for genomes of all sizes, virus to mammals
    • Learn the advantages of the different sequencing technologies e.g. Illumina, Pacific Bioscience and Oxford Nanopore for de novo assembly and how to access the quality of genomes sequences
    • Hands on experience of common tools for de novo sequence assembly, including visualization, contig ordering, scaffolding and error correction
    • Hands on experience of gene finding, including the use of RNA-Seq data
    • Being comfortable to assemble and annotate genomes
    Session content:[...]m-20/

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

    Here is the full list of our courses and Workshops:
    Surveys: Benchmark your pay in the 2019 Genomics Salary Survey
    Submitted by Eugene Mc Daid; posted on Monday, December 10, 2018


    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:[...]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:[...]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:
    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


    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.


    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.


    • 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


    • 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


    June 27-28, 2019
    Florence, Italy

    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 ( and Thomson Reuters. Papers will also be included in ACADEMIA.EDU ( and Google Scholar.


    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] or visit the Future of Education conference website.


    December 10-14, 2018
    IIIT-Delhi campus, Delhi, India

    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 (
    Room D173, Lower Lobby D

    The program of the 13th Workflows in Support of Large-Scale Science (WORKS) Workshop is now available (

    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)
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