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    March 4-8, 2024
    Live online (synchronous), max 18 participants
    Sessions from Monday to Friday, 13:00 to 17:00 (Madrid time zone)
    https://www.transmittingscience.com/courses/statistics-and-bioinformatics/introduction-bayesian-inference-practice/

    INSTRUCTORS

    Dr. Daniele Silvestro (University of Gothenburg, Sweden) and Tobias Andermann (University of Gothenburg, Sweden)

    COURSE OVERVIEW

    This course is based on the assumption that the easiest way to understand the principles of Bayesian inference and the functioning of the main algorithms is to implement these methods yourself.

    The instructors will outline the relevant concepts and basic theory, but the focus of the course will be to learn how to do Bayesian inference in practice. He will show how to implement the most common algorithms to estimate parameters based on posterior probabilities, such as Markov Chain Monte Carlo samplers, and how to build hierarchical models.

    He will also touch upon hypothesis testing using Bayes factors and Bayesian variable selection.

    The course will take a learn-by-doing approach, in which participants will implement their own MCMCs using R or Python (templates for both languages will be provided).

    After completion of the course, the participants will have gained a better understanding of how the main Bayesian methods are implemented in many programs used in biological research work. Participants will also learn how to model at least basic problems using Bayesian statistics and how to implement the necessary algorithms to solve them.

    Participants are expected to have some knowledge of R or Python (each can choose their preferred language), but they will be guided "line-by-line" in writing their script. The aim is that, by the end of the week, each participant will have written their own MCMC – from scratch! Participants are encouraged to bring their own datasets and questions and we will (try to) figure them out during the course and implement scripts to analyze them in a Bayesian framework.

    More information and registration at https://www.transmittingscience.com/courses/statistics-and-bioinformatics/introduction-bayesian-inference-practice/ or writing courses[at]transmittingscience.com

    Best regards,
    Sole
    Soledad De Esteban-Trivigno

    July 15, 2024 - July 18, 2024
    Shanghai, China
    https://ieeeaitest.com/wp-content/uploads/2023/12/CFP-6th-IEEE-AITest-2024.pdf

    CALL FOR PAPERS

    Artificial Intelligence (AI) technologies are widely used in computer applications to perform tasks such as monitoring, forecasting, recommending, predicting, and statistical reporting. They are deployed in a variety of systems, including driverless vehicles, robot-controlled warehouses, financial forecasting applications, and security enforcement and are increasingly integrated with cloud/fog/edge computing, big data analytics, robotics, Internet-of-Things (IoT), mobile computing, smart cities, smart homes, intelligent healthcare, and many more. Despite this dramatic progress, the quality assurance of existing AI application development processes is still far from satisfactory, and the demand for demonstrable levels of confidence in such systems is growing. Software testing is a fundamental, effective, and recognized quality assurance method which has shown its cost-effectiveness to ensure the reliability of many complex software systems. However, the adaptation of software testing to the peculiarities of AI applications remains largely unexplored and needs extensive research to be performed. On the other hand, the availability of AI technologies provides an exciting opportunity to improve existing software testing processes, and recent years have shown that machine learning, data mining, knowledge representation, constraint optimization, planning, scheduling, multi-agent systems, etc. have real potential to positively impact software testing. Recent years have seen a rapid growth of interest in testing AI applications as well as the application of AI techniques to software testing. This conference provides an international forum for researchers and practitioners to exchange novel research results, articulate the problems and challenges from practices, deepen our understanding of the subject area with new theories, methodologies, techniques, process models, impacts, etc., and improve the practices with new tools and resources.

    IMPORTANT DATES

    Abstract Registration Due: March 8, 2024
    Submission Deadline: April 1, 2024
    Notification Due: June 1, 2024
    Final Version Due: June 15, 2024
    Education: Hands-On NGS Data Analysis Workshops 2024
    Submitted by Dr. David Langenberger; posted on Saturday, January 20, 2024

    Submitter

    Check the upcoming hands-on NGS Data Analysis Workshops for 2024:

    February 28-March 1 (Online)
    Online Course - A Practical Introduction to NGS Data Analysis
    Link: https://www.ecseq.com/workshops/workshop_2024-01-A-Practical-Introduction-to-NGS-Data-Analysis-Online-Course

    March 11-14 (Berlin, Germany)
    RNA-Seq Data Analysis Workshop
    Link: https://www.ecseq.com/workshops/workshop_2024-02-RNA-Seq-data-analysis

    May 6-8 (Berlin, Germany)
    Single-Cell RNA-Seq Data Analysis: A Practical Introduction
    Link: https://www.ecseq.com/workshops/workshop_2024-03-Single-Cell-RNA-Seq-Data-Analysis

    May 27-29 (Online)
    Online Course - Bioinformatics Pipeline Development with Nextflow
    Link: https://www.ecseq.com/workshops/workshop_2024-04-Bioinformatics-Pipeline-Development-with-Nextflow-Online-Course

    June 10-14 (Berlin, Germany)
    8th Berlin Summer School 2024
    Link: https://www.ecseq.com/workshops/workshop_2024-05-8th-Berlin-Summer-School-NGS-Data-Analysis

    September 2-4 (Munich, Germany)
    Next-Generation Sequencing Data Analysis: A Practical Introduction
    Link: https://www.ecseq.com/workshops/workshop_2024-06-NGS-Next-Generation-Sequencing-Data-Analysis-A-Practical-Introduction

    September 25-27 (Leipzig, Germany)
    Single-Cell RNA-Seq Data Analysis: A Practical Introduction
    Link: https://www.ecseq.com/workshops/workshop_2024-07-Single-Cell-RNA-Seq-Data-Analysis

    November 13-15 (Online)
    Online Course - Bioinformatics Pipeline Development with Nextflow
    Link: https://www.ecseq.com/workshops/workshop_2024-08-Bioinformatics-Pipeline-Development-with-Nextflow-Online-Course

    December 9-11 (Online)
    Online Course - A Practical Introduction to NGS Data Analysis
    Link: https://www.ecseq.com/workshops/workshop_2024-09-A-Practical-Introduction-to-NGS-Data-Analysis-Online-Course

    Link to all courses: https://www.ecseq.com/workshops/ngs-data-analysis-courses
    Software: BIRCH Bioinformatics System v3.90
    Submitted by Brian Fristensky; posted on Monday, January 15, 2024

    Submitter

    BIRCH 3.90 now available for download at http://home.cc.umanitoba.ca/~psgendb/local/public_html/BIRCH3.90announcement.html

    NEW

    • BioLegato 1.1.2
    • New platform: macos-arm64 (eg. M1, M2, Apple Silicon)
    • Many updates to software packages
    • Full Python3 compliance
    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

    EXCERPT

    Today, the U.S. Food and Drug Administration approved two milestone treatments, Casgevy and Lyfgenia, representing the first cell-based gene therapies for the treatment of sickle cell disease (SCD) in patients 12 years and older. Additionally, one of these therapies, Casgevy, is the first FDA-approved treatment to utilize a type of novel genome editing technology [CRISPR/Cas9], signaling an innovative advancement in the field of gene therapy.
    Source: https://www.fda.gov/news-events/press-announcements/fda-approves-first-gene-therapies-treat-patients-sickle-cell-disease

    Submitter

    This article aims to instruct you on how to swiftly locate related sequences via a simple one-click method, using the target name.

    Taking HER2 target as an example, suppose you are very concerned about antibody drugs related to the HER2 target, and you want to inquire about the publicly available antibody sequences for the HER2 target worldwide. This article will teach you how to search for related sequences with one click through the target name.

    Learn more: https://synapse.patsnap.com/blog/how-to-obtain-target-related-sequences-directly-through-target-name-and-perform-sequence-alignment

    Exciting News!📚🔬

    I am thrilled to announce that my book proposal has been accepted by Springer Nature for an upcoming publication on cutting-edge topics in Bioinformatics. We are inviting passionate authors to contribute to this comprehensive work, covering various crucial areas such as Next-Generation Sequencing, Single-Cell Genomics, Machine Learning in Bioinformatics, and more.

    If you have groundbreaking research or insights to share in any of the chapters listed below, we would love to hear from you! 🌱🧬

    1. Introduction to Bioinformatics: Past, Present, and Future
    2. Next-Generation Sequencing and Genomic Data Analysis
    3. Single-Cell Genomics and Transcriptomics Analysis
    4. Metagenomics and Microbiome Analysis
    5. Structural Bioinformatics and Protein Structure Prediction
    6. Machine Learning and Artificial Intelligence in Bioinformatics
    7. Integrative Omics and Systems Biology
    8. Bioinformatics in Precision Medicine and Personalized Healthcare
    9. Drug Discovery and Repurposing through Bioinformatics
    10. Bioinformatics in Crop Improvement and Agricultural Genomics
    11. Immunoinformatics and Vaccine Development

    Don't miss the opportunity to be part of this book📕! The deadline for submissions is 31 March 2024. Let's push the boundaries of Bioinformatics together. 🚀 #Bioinformatics #ResearchOpportunity #SpringerNature #AcademicPublishing

    👉🏻Hurry up! Only chapter 11 is available.

    For any queries, please reply to spnaturebook[at]gmail.com

    Submitter

    November 24-26, 2023
    Vellore Institute of Technology
    Vellore, India
    https://vit.ac.in/school-bio-sciences-technology-sbst/indian-conference-bioinformatics-2023-inbix23-0

    Late-breaking abstracts end this Sunday. Join and experience the bioinformatics gala!

    Five reasons to attend Inbix2023: Indian Conference on Bioinformatics 2023:

    1. It is hosted by VIT, Vellore, the top 10 private universities in India taking leaps and bounds in research in the region, and organised by Bioclues.org, India's largest bioinformatics society working for Mentor-Mentee relationships.

    2. Scintillating keynotes and Life Time Achievement Awardees by revered Kenta Nakai, PB Kavi Kishor, PK Gupta and Jayaraman K Valadi and 18 other speakers across all states of India, some of the excellent speakers in the areas of #bioinformatics, #proteomics #machinelearning #genetics and #functionalgenomics

    3. Two panel discussions on "Millet Bioinformatics", elevator pitch and our unique video abstracts, all free for life members

    4. Have you ever heard of 12-17 year old children introduced to bioinformatics and coding? Yes, you guessed it right! We have our prestigious bioinformatics for school children (BIXS) programme through #Bioclues and this time as well, children will enthrall you with their works as we take you through students projects

    5. Team Bioclues #camaraderie through the three day event where we take pride in putting it and a preconference workshop on 23rd magnifies the spirit of bioinformaticshood!

    Come, join us! You will be missing something, if you haven't registered yet! What's more! The deadline for Late-breaking abstract submission ends soon: https://easychair.org/cfp/Inbix2023
    #research #event #india #coding #projects #bioinformatics

    Submitter

    Chimeric antigen receptor (CAR) T cell therapy, in which a patient's own T lymphocytes are engineered to recognize and kill cancer cells, has achieved remarkable success in some hematological malignancies in preclinical and clinical trials, resulting in six FDA-approved CAR-T products currently available in the market. Once equipped with a CAR construct, T cells act as living drugs and recognize and eliminate the target tumor cells in an MHC-independent manner.

    CARs are synthetic immune receptors that connect a single-chain variable fragment (scFv), derived from a monoclonal antibody to T cell signaling domains to eradicate tumor cells independent of the major histocompatibility complex (MHC).

    Once equipped with a CAR, T cells, known as CAR-T cells, act as living drugs and recognize and eliminate the target tumor cells. The conventional CAR structure consists of three modular components: the ectodomain, the transmembrane domain, and the endodomain, each of which has specific components and functions and thus the potential to be optimized.

    An exemplification using Tisagenlecleucel demonstrates the approach of performing sequence retrieval for each individual region, as well as searching for the overall relevant sequence through a combination of different fragments.

    Continue reading: https://synapse.patsnap.com/blog/car-t-core-functional-component-sequence-retrieval-strategy

    Empowering Researchers with Advanced End-to-End Analysis Tools for Single-Cell and Genetic Variation Studies.

    BioBam, the leading bioinformatics software company, is pleased to announce OmicsBox 3.1, its latest version packed with innovative features designed to empower researchers, scientists, and bioinformaticians in their pursuit of advanced omics data analysis and interpretation.

    OmicsBox has consistently led the way by providing comprehensive genomics, transcriptomics, and metagenomics data analysis tools. This release represents a significant step forward, introducing new Single-Cell analysis capabilities, strengthening Long-Read transcriptome analysis, and enhancing Genetic Variation analysis.

    Dr. Stefan Götz, CEO, stated, "With the latest release, OmicsBox now offers an exceptionally flexible analysis solution for Single-Cell RNA-Seq data, addressing the unique challenges presented by this rapidly evolving field. We anticipate that these new features will build on the success of other OmicsBox modules and make Single-Cell data analysis more accessible to the broader community."

    In OmicsBox 3.1, the Single-Cell Data Analysis capabilities have been enhanced to support Expression Quantification tailored for UMI-based technologies like 10x Genomics Chromium and Drop-seq. The additions now enable end-to-end analysis of sequencing reads, from quantification to in-depth analysis, including clustering, trajectory analysis, and functional interpretation.

    In the Long-Read Transcriptome data analysis, OmicsBox 3.1 introduces a new read aligner, complementing well-established tools like Flair, IsoSeq, and Sqanti. This unifies all the essential tools for PacBio or ONT long-read data analysis in a single, user-friendly platform.

    The Genetic Variation Module has also received updates introducing an end-to-end solution for genetic variation analysis, featuring a cutting-edge functional enrichment tool designed exclusively for genome-wide association studies (GWAS). Additionally, support for mixed ploidy and interactive Manhattan plots has been included.

    About OmicsBox:

    OmicsBox is a leading bioinformatics solution that offers end-to-end data analysis of genomes, transcriptomes, metagenomes, and genetic variation studies. The application is used by top private and public research institutions worldwide and allows researchers to easily process large and complex data sets, and streamline their analysis process. It is designed to be user-friendly, efficient, and with a powerful set of tools to extract biological insights from omics data.

    The software is structured in different modules, each with a specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results. The functional analysis module, which includes the popular Blast2GO annotation methodology makes OmicsBox particularly suited for non-model organism research. Over 25k scientific research citations demonstrate this. OmicsBox works out of the box on any standard PC or laptop with Windows, Linux, or Mac. You can also explore its features with a free trial, making it even more accessible for students and researchers. https://www.biobam.com/trial/

    About BioBam:

    BioBam is a leading bioinformatics company that provides innovative software solutions to accelerate genomics research. The company is dedicated to developing user-friendly and powerful bioinformatics tools that simplify data analysis for researchers, empowering them to focus on data interpretation and explore new insights. BioBam aims to close the technology gap between state-of-the-art bioinformatics and applied genomics research, by transforming complex data analysis into intuitive and interactive tasks that facilitate scientific advancement.

    Follow BioBam on LinkedIn, Twitter, Facebook, and YouTube.

    Contacts:

    Stefan Götz, CEO
    BioBam Bioinformatics S.L.
    sgoetz[at]biobam.com
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    Acknowledgments

    We wish to thank the following for their support:

    [University of Birmingham]
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