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    Submitter

    Would you like to see an interactive virus capsid model quickly and easily? Slab it or cut it in half? A clathrin coat? A bacterial gas vesicle? The mysterious "vault" eukaryotic nanocompartment?

    https://proteopedia.org/w/FirstGlance/Virus_Capsids_and_Other_Large_Assemblies

    The views at the above link were obtained with Version 4.0 of FirstGlance in Jmol released August 15, 2022 (free and open source; google "firstglance" as one word, or http://firstglance.jmol.org). Newly, it automatically constructs "biological assemblies" and shows "biomolecule 1" in its initial view. Exploring the asymmetric unit is then an option.

    Very large assemblies+++ are automatically simplified to alpha carbons, or a subset of alpha carbons; see examples at the above link. What are such simplified models good for? They can be measured, colored by secondary structure, hydrophobic/polar, charge, amino-to-carboxy rainbow, or evolutionary conservation (if pre-processed by the ConSurf Server). Each group of sequence-identical chains can be assigned a distinct color (under Solid in the Views tab).

    You can make an animation, ready to drop into a presentation slide, from any view in FirstGlance. It takes just a few mouse clicks. Examples in Google Slides:

    http://tinyurl.com/movingmolecules

    A small assembly, 2acz, has 4 chains in its asymmetric unit, and 12 chains in its biomolecule 1. You will be offered the option to simplify, so you can try it both ways. Even simplified to alpha carbons, the transmembrane helices stand out with the hydrophobic/polar and charge views. Its construction can be understood by giving a distinct color to each of the 4 sequence-distinct protein chains (Solid in the Views tab).

    http://firstglance.jmol.org/fg.htm?mol=2acz

    Structural biologists: With FirstGlance, you can't miss (after clicking "Show more details") incomplete sidechains, missing residues, alternate locations (can be animated), occupancy < 1.0 (all exemplified in 1ijw). All salt bridges can be displayed with one click (Tools tab), and a spreadsheet-ready list is reported with one more click. A "Contacts & Non-Covalent Interactions" tool makes it easy to visualize the interactions with any moiety you specify. Protein crosslinks are automatically detected and highlighted/zoomed with a few clicks: isopeptides, thioesters, thioethers, his-tyr, lys-cys NOS as well as, of course, disulfides. Step by step:

    https://proteopedia.org/w/FirstGlance/Evaluating_Protein_Crosslinks

    Electron density maps (or EM density maps) can be displayed for anything selected with the Find.. dialog, as well as crosslinks and ends of chains. See examples from FirstGlance here:

    https://proteopedia.org/w/Electron_density_maps

    New color schemes for simplified models:

    http://firstglance.jmol.org/notes.htm#bucolors

    New color schemes for simplified models:

    http://firstglance.jmol.org/notes.htm#bucolors

    To clear the old version of FirstGlance out of your browser's cache, go to

    http://firstglance.jmol.org/fg.htm?mol=1ijw

    Then regardless of whether the molecule displays, hold down the Shift key while you Reload.

    +++"Very large assemblies" means >25,000 non-hydrogen atoms. Only about 3% of entries in the World-Wide Protein Data Bank have biological assemblies that large. However, these include very important structures, such as virus capsids. Simplification rules:

    http://firstglance.jmol.org/notes.htm#simplification
    Events: EDGE: A global undergraduate STEM conference
    Submitted by Frank Lee; posted on Friday, August 12, 2022

    15 November 2022
    Location: Hybrid
    https://www.edge-stem.org

    EDGE is a global non-profit undergraduate conference, which welcomes submissions of student research from all areas of STEM. The overarching aim of this conference is to give students a platform where they are able to showcase their original research in different STEM fields, encourage dialogue, and thereby promote the practice of STEM research more generally. Furthermore, by inviting established researchers in different fields as keynote speakers, we look to provide an opportunity for students to learn about the value and inner workings of academia, and grow their academic network.

    REGISTRATION

    Registration is free and special awards await the best paper, best presentation, and best researcher at the conference.

    TOPICS OF INTEREST

    Any papers related in STEM areas are welcome. We are especially looking forward to papers related to the following areas:
    • Applied sciences
    • Biological sciences
    • Computer science
    • Health sciences
    • Physical sciences
    • Neuroscience
    • Mathematics

    IMPORTANT DATES

    Deadline for abstract submission: 31 August 2022
    Deadline for paper submission: 20 September 2022
    Notification of acceptance: 20 October 2022
    Conference date: 15 November 2022

    GUIDE FOR AUTHORS

    • Please limit your abstract to 300 words.
    • The paper must adhere to any of the standard citation formats. It must have a word limit of 5000 words. The format for the file name is LASTNAME.FIRSTNAME.SUBJECT-AREA.TITLE (e.g. Smith.Bob.Biology.The Evolution of Tool Use in Primates).
    • Submit your abstract and paper to submission[at]edge-stem.org.
    • Each participant is given 15 minutes to present their paper. There will be a 5-minute Q&A portion after the presentation. Everyone is encouraged to use a slide deck which must be sent to the organizing committee prior to the conference.

    FOR MORE INFORMATION

    For all general inquiries, please contact: submission[at]edge-stem.org.

    Submitter

    August 7-9, 2022
    Philadelphia, PA, USA
    https://icibm2022.iaibm.org

    Dear Colleagues:

    The 10th International Conference on Intelligent Biology and Medicine (ICIBM 2022) will take place Philadelphia, PA, USA August 7-9, 2022, https://icibm2022.iaibm.org. 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.

    Our keynote include Drs. Xihong Lin, Ludmil Alexandrov, Smita Krishnaswamy, Mona Singh. Eminent Scholars includes:Drs. Feixiong Cheng, Jiang Qian, Yuan Luo, Li Shen, Derrick Scott, Lana Garmire.

    Registration is open. Please join us.

    ICIBM 2022 Organization Committee

    The web service Hiplot has been published in the journal Briefings in Bioinformatics.

    ABSTRACT

    Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud-and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publication-ready graphics that allow easy scaling and updatability according to user demands. Therefore, we propose a community-driven modern web service, Hiplot (https://hiplot.org), with concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, to improve the efficiency in use and development of plugins, we introduced some core advantages on the client-/server-side of the website, such as spreadsheet-based data importing, cross-platform command-line controller (Hctl), multiuser plumber workers, JavaScript Object Notation-based plugin system, easy data/parameters, results and errors reproduction and real-time updates mode. Meanwhile, using demo/real data sets and benchmark tests, we explored statistical parameters, cancer genomic landscapes, disease risk factors and the performance of website based on selected native plugins. The statistics of visits and user numbers could further reflect the potential impact of this web service on relevant fields. Thus, researchers devoted to life and data sciences would benefit from this emerging and free web service.

    CITATION

    Jianfeng Li et al. "Hiplot: a comprehensive and easy-to-use web service for boosting the publication-ready biomedical data visualization." Briefings in Bioinformatics, bbac261 (2022). https://doi.org/10.1093/bib/bbac261.

    AVAILABILITY

    Website: https://hiplot.org

    Submitter

    We are happy to announce a new web server and standalone software, HLAncPred, developed for predicting non-classical HLA binders.

    Web server link: https://webs.iiitd.edu.in/raghava/hlancpred/

    Paper link: https://doi.org/10.1093/bib/bbac192

    Submitter

    December 6-9, 2022
    International Conference on Bioinformatics and Biomedicine (BIBM 2022)
    Las Vegas, NV, USA
    https://ieeebibm.org/BIBM2022/

    Network Science and Artificial Intelligence for Biomedicine & Health informatics (NSAIBHI) Workshop:
    Network Science is a new paradigm of study to understand complex systems including biological interactions. Pharmacology and drug discovery leverage network biology advances for a better understanding of the complex interactions between drugs, targets and disease, for designing new molecule, and for identifying drugs to be successfully repurposed. More recently, graph neural networks expressed to be a potential game changer in deciphering the inherent complex interaction patterns in complex networks.

    The workshop and the foreseen special issue intend to highlight novel research in the area of network science, network biology and network medicine coupled with representation learning and its application to biology, medicine, and pharmacology. The focus is on, but not limited to, the following broad areas:

    1. Network Representation Learning
    2. Graph Convolution Neural Network
    3. Network Embedding
    4. Heterogeneous network integration
    5. Network Alignment
    6. Disease module detection
    7. Network Drug Discovery and Repurposing

    IMPORTANT DATES

    Electronic submission of full papers: Aug, 21, 2022
    Notification of paper acceptance: Oct 21, 2022
    Main conference Camera-ready of accepted papers: Nov 12, 2022
    Workshop Paper Camera-ready of accepted papers: Nov 12, 2022
    Conference: Dec. 6-9, 2022

    PROCEEDINGS

    All workshop accepted papers and posters will appear in the IEEE Conference Proceedings.

    A special issue on a Scopus Indexed Journal is planned, negotiations are in progress, journals will be communicated in an upcoming announcement.
    Software: BIRCH Bioinformatics System v3.86
    Submitted by Brian Fristensky; posted on Saturday, June 11, 2022

    Submitter

    BIRCH 3.86 now available for download at http://home.cc.umanitoba.ca/~psgendb/local/public_html/BIRCH3.86announcement.html

    NEW

    • Important fix to OSX BIRCH launcher
    • Sequence database search improvements
    • Application updates
    BIRCH unifies hundreds of popular bioinformatics tools through the BioLegato family of Object-Oriented applications. BioLegato makes it easy to try out new programs, and to experiment with your data at every step in the analytical process.

    Visit our YouTube Channel at https://www.youtube.com/channel/UC9_3TfH3sjE0YdToVMChq-w?view_as=public

    Submitter

    Healthcare is generating and collecting huge amounts of data from electronic health record systems, medical imaging, lab data and genomics testing. Tools and methods are currently being developed to improve our ability to analyze and understand this abundant amount of health data. Through the correct application of tools and methods, we can improve patient outcomes and reduce costs. Professionals with this ability are increasingly in high demand.

    The mission of Georgetown University's Health Informatics and Data Science program (https://healthinformatics.georgetown.edu) is to equip our students with cutting-edge techniques, to give them a firm grasp on methodologies and to be highly qualified for the market. It is designed to help students develop core competencies in data science, health-related data, predictive analytics, machine learning (ML), Artificial Intelligence (AI) and other advanced technologies. Through the program, students will be prepared to successfully take on a wide range of opportunities in health care organizations and related industries including, health technology developers, device manufacturers, pharma/biotech, academic medical centers and management consulting firms. We help our students build critical skills for this growing sector to lead the evolution of healthcare.

    Through multi-disciplinary coursework and projects, HIDS students will be exposed to, and interact with, field experts, peers and faculty from top-ranked Georgetown University departments. Our unique Georgetown experience prepares the next generation of health informaticians to lead and make a difference in patient care and population health.

    Make your career move now! Come talk to us about how Georgetown's Health Informatics & Data Science fits into your academic and professional goals! Please visit https://bit.ly/3qqHB2r.

    Georgetown-HIDS is a proud member of the AI/ML Consortium to Advance Health Equity & Researcher Diversity (AIM-AHEAD) Program (https://datascience.nih.gov/artificial-intelligence/aim-ahead).

    June 13-15, 2022
    Hotel Le Méridien, 20 Sidney St, Cambridge, MA, USA
    https://www.biscglobal.com/training/bioinformatics-biostatistics-and-machine-learning-techniques-for-biotech-applications/

    We are pleased to announce that the registration for our training "Bioinformatics, Biostatistics and Machine Learning Techniques for Biotech Applications" has been opened.

    If you want to learn about the latest techniques and applications of bioinformatics, statistics and ML in life science, you can find out more and register on the website listed above.

    During this 3-day hands-on training in Boston you will learn about:
    • NGS data analysis (Day 1)
    • Introduction to Biostatistics of Clinical Trials (Day 2)
    • Machine Learning (Day 3)
    Takeaway: You will learn about the most in-demand bioinformatics, biostatistics and machine learning techniques you need to succeed as a bioinformatician or data scientist in the biotech industry. For each pipeline and model, you will learn how it works conceptually first, then apply it to a particular industrial application, and finally learn to analyze and visualize the results.

    Registration: Secure your spot now. Seats are limited, and we accept applicants on a first-come, first-served basis.

    Submitter

    There's a lot to be impressed about when considering a career in bioinformatics.

    First, it's one of the most multidisciplinary fields of science, merging not just computing and biology but also drawing on methods from mathematics, engineering, physics and chemistry.

    Second, bioinformaticians are at the bleeding edge in applied computing, making use of artificial intelligence, Big Data and cloud computing to treat diseases and advance our understanding of life. In fact, many of the most powerful supercomputers in the world are used to solve bioinformatics problems.

    In the future, bioinformatics will bring personalized healthcare through the rapid and inexpensive analysis of a patient's whole genome, which can be ordered at their doctor's office. The future will also bring new therapies designed by artificial intelligence, cutting years off of development time.

    At the University of Birmingham you can be on your way to such an exciting and impactful career. Their flexible, 100% Online MSc Bioinformatics connects biology, clinical services, mathematics, and computer science, giving students the knowledge they need to respond to growing healthcare challenges.

    The university is now accepting Summer 2022 applications. Request more information to find out how to apply (https://bit.ly/34rUQIy).
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    Acknowledgments

    We wish to thank the following for their support:

    [University of Glasgow]
    [Bio-IT World]
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