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    Submitter

    I've written a new guide:

    How to find the structure of a protein: https://proteopedia.org/w/How_to_find_the_structure_of_a_protein. Its suitable for students. It starts by finding the amino acid sequence in UniProt, and suggests what to consider when selecting the best model when multiple empirical models are available. And when no empirical model is available, it directs you to ...

    How to predict structures with AlphaFold using the newest AlphaFold3 Server (with a few tips to avoid frustration): https://proteopedia.org/w/How_to_predict_structures_with_AlphaFold

    There is also a new guide about how to be aware of Missing Residues and Incomplete Sidechains: https://proteopedia.org/w/Missing_residues_and_incomplete_sidechains. It illustrates how you can't be unaware of them in FirstGlance in Jmol, but you may well be unaware in MolStar, PyMOL, ChimeraX, or iCn3D. Then it suggests how to use AlphaFold models to fill in missing sidechain atoms or loops, so that your analysis of charge distribution is not erroneous.

    Filling in missing charged atoms on the protein surface is especially important before you make an Electrostatic Potential Map, which you can do quite easily in several popular free applications: https://proteopedia.org/w/Electrostatic_potential_maps. That new page illustrates maps made in each application.

    ~ Eric Martz http://martz.molviz.org

    Submitter

    November 26, 2024
    19:30 hrs IST (0900 hrs ET)

    At The Forefront of Genomics: Making Genomic Medicine a Reality
    Eric Green, MD, PhD
    Director, NHGRI, USA

    Moderated by: Prashanth N Suravajhala, PhD and Gyaneshwer Chaubey, PhD

    One-click registration at https://bioclues.org/events

    Submitter

    "Body roundness index (BRI) might be a more accurate measurement than body mass index (BMI) for predicting weight-related health risks."

    Source: https://www.health.harvard.edu/staying-healthy/body-roundness-may-beat-body-mass-for-identifying-risky-fat

    Journal article: https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2819558

    Submitter

    March 19, 2025 (online event)
    March 20-21, 2025 (in Florence, Italy)
    http://conference.pixel-online.net/NPSE/callforpapers.php

    The event brings together teachers, researchers, practitioners and project managers from all over the world to share findings, expertise and experience about innovative science teaching and learning methodologies.

    Onsite participants are welcome in Florence for two full days of thought-provoking sessions, integrated by endless networking opportunities and social events.

    Online participants can contribute with asynchronous or synchronous online presentations. The latter will be delivered on 19 March via the Conference Virtual Platform.

    During the Conference:
    • All accepted papers will be presented onsite and online.
    • Questions and Answers sessions will follow each paper presentation.
    • Poster presentation sessions will be held onsite and online.
    • Networking opportunities will be organized.

    IMPORTANT DATES

    Abstracts submission deadline: October 9, 2024
    Papers submission (possibility to extend): January 22, 2025
    Conference day of the ONLINE EVENT: March 19, 2025
    Conference days of the ONSITE EVENT IN FLORENCE: March 20-21, 2025

    All accepted papers will be included in the Conference Proceedings e-book published with ISBN, ISSN and DOI codes. The publication will be sent to be reviewed for inclusion Web of Science and SCOPUS. The publication will also be included in Academia.edu and indexed in Google Scholar.

    FOR MORE INFORMATION

    Contact: science[at]pixel-online.net
    Video: https://youtu.be/EtINTHNZyjE

    Submitter

    Creative Biolabs, a leading CRO, is proud to announce the opening of applications for its 2024 scholarship program. This initiative aims to provide financial assistance to students within the biotechnology industry, supporting their academic pursuits and research endeavors.

    The Creative Biolabs Scholarship Program reflects the company's commitment to nurturing the next generation of biotech talent. As a renowned provider of biopharmaceutical development solutions, Creative Biolabs recognizes the importance of investing in the education and advancement of young scientists and researchers.

    "We are excited to launch our 2024 scholarship program, which underscores our dedication to fostering innovation and excellence in the field of biotechnology," according to a scientist at Creative Biolabs. "Through this initiative, we aim to empower students to pursue their academic and professional aspirations, ultimately contributing to the advancement of the biotech industry."

    The scholarship program opens to undergraduate, graduate, and doctoral students pursuing studies in science-related fields, with a focus on areas such as immunology, biochemistry, and molecular biology, which play a crucial role in the development of novel biopharmaceuticals and are key areas of focus for Creative Biolabs. Applicants will be evaluated based on academic merit, research achievements, leadership potential, and a personal statement outlining their career goals and aspirations in biotechnology.

    "In addition to financial support, the recipients of the Creative Biolabs Scholarship have the chance to learn more about the exclusive resources and networking opportunities within the biotech community. This includes access to Creative Biolabs' cutting-edge technologies and platforms, such as high-throughput hybridoma generation, B cell sorting, and de novo antibody sequencing." The scientist elaborated.

    High-Throughput Hybridoma Generation:

    One of the key technologies offered by Creative Biolabs is the powerful Hyperdoma™, by far the most comprehensive and advanced hybridoma generation and screening platform, incorporating high-throughput screening systems like ClonePix 2, FMAT, and Celigo Image Cytometer. It fully takes advantage of the hybridoma machinery to sift out the best antibodies for any possible research, and meanwhile, its electrofusion and advanced screening approaches generate an expanded positive clone pool to largely maximize the possibility of producing the most viable clone, essential for the production of monoclonal antibodies. Utilizing this technology, researchers can significantly accelerate the process of antibody development and maximize their research efficiency.

    De Novo Antibody Sequencing:

    Another important solution is de novo antibody sequencing, which achieves 100% accuracy in interpreting antibody sequences and covers V, J, and C gene segments, the CDR3 region, fluorochrome mAbs and non-standard antibodies, and isobaric amino acids.

    "Our scholarship recipients will have the opportunity to engage with industry-leading experts and learn more about state-of-the-art technologies like those above to further their research endeavors," said the scientist. "We believe that by investing in the education and development of talented students, we can drive innovation and advance the frontiers of biotechnology."

    Interested students can find more information and apply for the scholarship program at https://www.creative-biolabs.com/scholarship-program.html.

    ABOUT US

    Creative Biolabs, specializing in biopharmaceutical development, offers a range of antibody discovery services. With a focus on nurturing talent, Creative Biolabs annually provides scholarships to biotech students, reflecting its dedication to education and innovation.
    Resources: Prediction of Toxicity of Peptides
    Submitted by Gajendra P.S. Raghava; posted on Thursday, July 25, 2024

    Submitter

    We are happy to announce updated version of our popular web server ToxinPred, which is developed for predicting for predicting toxicity of peptides. This will be useful for researchers who's working on peptide-based drug discovery.

    URL: http://webs.iiitd.edu.in/raghava/toxinpred3/
    Paper Link: https://www.sciencedirect.com/science/article/pii/S0010482524010114?dgcid=author
    Education: Creative BioMart Scholarship Program 2024
    Submitted by Caroline Green; posted on Thursday, July 25, 2024

    As a leading supplier of a wide range of biological products including recombinant proteins, native proteins, cell/tissue lysates, etc. and a high-quality custom service provider specializing in academic research, diagnostic and therapeutic applications as well as industry requirements, Creative BioMart always strives to support young and ambitious talents in our field.

    To further support their research and higher education in the biomedical and science fields, Creative BioMart is proud to announce the 2024 Scholarship Program, which will award $1,000 to an outstanding college student.

    Thanks for your interest in the 2024 Creative BioMart Scholarship Program!

    REQUIREMENTS

    The Creative BioMart scholarship is open on a global basis. To be eligible to receive a scholarship, you must meet the following requirements:
    • Enrolled as an undergraduate, graduate or Ph.D. student at an accredited college, university or research Institute.
    • Major in Biology, Biochemistry, Molecular Biology, Biotechnology or a related major.
    • Can provide proof of a good average grade with at least a B (GPA 3.0/4.0).

    EVALUATION CRITERIA

    The Creative BioMart selection committee will review each application fairly and carefully according to the following criteria:

    Academic ability: In addition to grade point average, your project, Bachelor's/Master's thesis, internship experience, or detailed learning plan will be considered.
    Leadership skills: The ability to organize and positively influence others inside and outside of school.
    Social concerns: Purposeful and meaningful participation in volunteer activities, community service or other public service activities.

    FOR MORE INFORMATION

    More at https://www.creativebiomart.net/creative-biomart-scholarship-program-2024.htm

    Submitter

    October 10-12, 2024
    Houston, TX, USA
    https://icibm2024.iaibm.org

    We are pleased to announce the 12th International Conference on Intelligent Biology and Medicine (ICIBM 2024), which will take place in Houston, TX, USA. ICIBM is a high-caliber conference that brings together eminent scholars with expertise in various fields of computational biology, systems biology, computational medicine, and experimentalists interested in the 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 and abstracts with unpublished, original work describing recent advances in all aspects of Bioinformatics, Intelligent Computing, Systems Biology, and Medical Informatics, including but not restricted to the following topics:

    Bioinformatics:
    • Genomics and genetics/epigenetics, including integrative & functional genomics, genome evolution, GWAS.
    • Next-generation sequencing data analysis, 3D genome.
    • 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, function, and interactions.
    • Single-cell sequencing data analysis.
    • Microbiome and Metagenomics.
    Intelligent Computing and Data Science:
    • Artificial intelligence, machine learning, deep learning, data mining, knowledge discovery.
    • Large language model, foundation model, and computer vision in biomedical.
    • Natural language processing, literature mining, semantic ontology, and health informatics.
    • Neural computing, kernel methods, feature selection/extraction.
    • Evolutionary computing, swarm intelligence / optimization, ensemble methods.
    • Artificial life and artificial immune system.
    • Biomedical image analysis and processing.
    Systems Biology:
    • Modeling and simulation of biological processes, pathways, networks, and interactomes.
    • Modeling of cellular and multi-cellular interaction systems.
    • Multi-dimensional omics data integration.
    • Synthetic biological systems.
    • Metabolomics, microbiome, and lipidomics.
    • Self-organization in living systems (cells, organisms, swarms, ecosystems, etc.).
    Medical Informatics:
    • Cohort discovery, EHR-based phenotyping, predictive modeling.
    • Data quality assessment or validation.
    • Clinical decision support solutions.
    • Informatics to address disparities in health and health care.
    • Interoperability (e.g., ontology, terminology, standards, and others).
    • Machine learning for clinical applications, genome, and phenome analysis/associations.
    • Mobile health and wearable devices.
    • Human-computer interaction and human factors
    Paper Submission and Publication:

    Prospective authors are invited to submit unpublished work to ICIBM 2024. All papers and abstracts will be initially submitted through the EasyChair Conference System. Selected papers of the registered authors will be recommended to be published in special issues in the following journals, subject to additional editorial approval and expected additional review by each journal: Patterns (impact factor: 6.5), Computational and Structural Biotechnology Journal (CSBJ, impact factor: 6.0), International Journal of Molecular Sciences (IJMS, impact factor: 5.6), Quantitative Biology (impact factor 3.1), Information (impact factor 3.1), Cancers (impact factor 5.2).

    Abstract Submission:

    Conference participants are invited to submit abstracts to ICIBM 2024. Abstract submitted to the conference should be formatted using the Abstract Template. The abstract body should be no more than 400 words. We welcome submissions of highlight papers that have been recently published or accepted for publication. In this case, the abstract should include a complete reference to the published paper. A group of experts will evaluate the submissions and select the abstracts to be presented orally or as a poster. Please submit your abstract to icibm2024.abstract[at]gmail.com.

    Travel Awards:

    The Travel Award, which pending on a grant application, is to encourage young scientists in training, including graduate, undergraduate and high school students, as well as postdoctoral fellows. Specific consideration will be given to qualified applicants from underrepresented populations, minority institutes, female trainees, or those who needs special financial support to attend ICIBM 2024.

    IMPORTANT DATES

    Deadline for original paper submission: July 5 (Fri), 2024
    Notification to authors of papers: August 23 (Fri), 2024
    Deadline for abstract submission: August 30 (Fri), 2024
    Conference early registration opens: June 20 (Thurs), 2024
    Conference early registration deadline: September 10 (Tues), 2024
    Deadline for travel award application: September 11 (Wed), 2024
    Conference regular registration: September 11 – October 10, 2024
    Research: A genomic language model (gLM) artificial intelligence
    Submitted by J.W. Bizzaro; posted on Thursday, April 04, 2024

    Submitter

    In a new Nature Communications article, researchers describe a genomic language model (gLM) capable of predicting protein co-regulation and function. The gLM, which was trained on millions of metagenomic scaffolds, has learned to interpret the language of genes, revealing the intricate dance of protein regulation and enzymatic functions. This approach is a leap forward in our understanding of the genomic blueprint and its regulatory networks.

    CITATION

    Hwang, Y., Cornman, A.L., Kellogg, E.H. et al. Genomic language model predicts protein co-regulation and function. Nat Commun 15, 2880 (2024). https://doi.org/10.1038/s41467-024-46947-9
    Proteopedia.Org Seeks Help
    Submitted by Eric Martz; posted on Wednesday, April 03, 2024

    Submitter

    https://Proteopedia.Org needs a major upgrade. Proteopedia.org (free, open source) was created in 2007 as a wiki encyclopedia of protein molecular structure incorporating JSmol (http://Jmol.Org). It is by far the easiest place to create customized interactive molecular scenes, which are then immediately online for anyone to see. "Green links" illustrate statements in text with interactive molecular scenes in JSmol. Proteopedia's pages have been visited >230 million times. Users have authored thousands of articles, >100 of which have been visited >50,000 times each. Professors and students are major users, as well as researchers. Over 5,000 people have set up free accounts. A brief introductory overview of Proteopedia is here:

    https://proteopedia.org/w/Proteopedia:Overview

    Rejuvenation will involve upgrading the obsolete versions of linux, MySQL, and Wikimedia that it now runs with on Amazon Web Services, and making all its customized features work with the new infrastructure. Those features include support to run JSmol within Wikimedia, the Scene Authoring Tools (https://www.youtube.com/watch?v=90jonYOzzCY), green links, etc. Then the content in the present implementation could be imported into the new system using an automated script that would also need to be developed. Jaime Prilusky, who created most of the present system and has maintained it until now, would very much like help from someone familiar with the components of the infrastructure, especially current MySQL. Limited funding may be available.

    Thanks from the Proteopedia Team, https://proteopedia.org/w/Proteopedia:Team
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