Register event
12 events found

Content provider: University of Cambridge Bio...  or de.NBI 

  • BioC++ - solving daily bioinformatic tasks with C++ efficiently - ISMB 2020

    12 July 2020

    BioC++ - solving daily bioinformatic tasks with C++ efficiently - ISMB 2020 https://tess.elixir-europe.org/events/bioc-solving-daily-bioinformatic-tasks-with-c-efficiently-ismb-2020 Educators: René Rahn, Marcel Ehrhardt, Svenja Mehringer (CIBI) Date: 12.07.2020 9:00 am - 1:00 pm (Eastern Daylight Time) Location: ISMB 2020: Virtual Conference https://www.iscb.org/ismb2020/4399 Contents: In this half-day tutorial we are going to teach how to use modern C++ and utilise modern C++ libraries to rapidly develop tools and scripts for operating on and manipulating large-scale sequencing data. The high variability and heterogeneity often observed within various genomic data is challenging for many standard tools, for example for read alignment and variant calling. Often, these tools are wrapped in complicated pre- and postprocessing data curation steps in order to obtain results with higher quality. However, these additional steps incur a high maintenance and performance burden to the established work process and often do not scale with larger data sets. Seldomly, C++ is considered as the language of choice for these small processes, although it is the main language used in high-performance computing. We are going to show that implementing modern C++ can be as easy as using other modern high-level languages. Learning goals: Students will develop - skills in developing an application using the C++ programming language - skills in using modern C++ libraries to query large sequence databases (e.g. SeqAn, SDSL, etc.) - knowledge and understanding of modern C++ features, such as ranges and concepts - knowledge and understanding about modern and efficient data structures as well as algorithms crucial for large-scale genomic sequence analysis - knowledge and understanding about how to develop and sustain high-quality software Prerequisites: This tutorial is mostly suited for computational biologist and bioinformaticians with research focus on sequence analysis (e.g., genomics, metagenomics, proteomics, read alignment, variant detection, etc.). A fundamental knowledge about sequencing experiments and the involved data is required. We expect that attendees have an intermediate knowledge in programming with any high-level programming language, e.g. Python, Java or C++. Some basic C++-knowledge is helpful but not mandatory to successfully complete the course. This tutorial is targeting beginners and intermediate C++ developers that want to learn more about modern C++ features like ranges and concepts. Keywords: BioC++, modern C++, bioinformatics, SeqAn, FileIO Tools: - A simple text editor - g++ >= 7 - cmake >= 3.12 - git 2020-07-12 09:00:00 UTC 2020-07-12 13:00:00 UTC de.NBI [] [] [] meetings_and_conferences [] []
  • An Introduction to Solving Biological Problems with Python (ONLINE LIVE TRAINING)

    13 - 14 July 2020

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with Python (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-python-online-live-training-80e28bc7-9c00-4d53-8652-0b814c574e74 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs. Course materials are available [here](http://pycam.github.io/). Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Concepts and strategies for working more effectively with Python are now the focus of a new 2-days course, [Data Science in Python](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-dspyt/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3503210&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python).'' 2020-07-13 08:30:00 UTC 2020-07-14 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Introduction to Galaxy and Python with Jupyter Notebook

    13 - 27 July 2020

    Introduction to Galaxy and Python with Jupyter Notebook https://tess.elixir-europe.org/events/introduction-to-galaxy-and-python-with-jupyter-notebook Educators: Julia Scheel, Andrea Bagnacani, Markus Wolfien (RBC) Location: Online Dates: 13.07.2020, 15.07.2020, 27.07.2020 Contents: Life sciences used to be all about wet-lab expertise. Due to fast technical innovations and digitalisation we are now facing the challenge of dealing with vasts amounts of data. Analyses of such data requires advanced statistics and specialized tools to run analyses and to visualize both data and results. Science becomes more and more dependent on bioinformaticians and computer scientists, which creates the additional challenge of interdisciplinary communication. This course introduces the Galaxy framework, an open source, web-based platform for data intensive biomedical research, Python, an interpreted, high-level, general-purpose programming language, and Jupyter Notebook, a multi-language framework for interactive computing. You can chose to use this course as a stepping stone into advanced analyses, or as an opportunity to learn what your bioinformatician of trust is actually doing. Further courses and tutorials for Galaxy and Python are widely available. Both Galaxy and Python have active user communities, making self-paced learning possible. Learning goals: - Know your data: implications of quality control and data preprocessing - Hands-on quality control and data preprocessing - Understanding and programming in Python - Hands-on session with Jupyter Notebooks. Prerequisites: This workshop is intended for PhD students with a background in medicine, engineering and life science research. In order to take part in the hands-on session we recommend one Laptop/PC and a stable internet connection. We further ask you to create a Galaxy account beforehand. Tools: - Galaxy: https://usegalaxy.eu - Python: https://python.org - Jupyter Notebook: https://jupyter.org/ 2020-07-13 09:00:00 UTC 2020-07-27 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • An Introduction to Machine Learning (ONLINE LIVE TRAINING)

    15 - 17 July 2020

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Machine Learning (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/an-introduction-to-machine-learning-online-live-training PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3513753&course-title=An%20Introduction%20to%20Machine%20Learning).'' 2020-07-15 08:30:00 UTC 2020-07-17 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Data mining University of Cambridge Bioinformatics Training [] This is aimed at life scientists with little or no experience in machine learning and that are looking at implementing these approaches in their research.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • KNIME: Practical introduction to KNIME Analytics platform and its application in bioinformatics (Webinar)

    29 - 30 July 2020

    Cambridge, United Kingdom

    Elixir node event
    KNIME: Practical introduction to KNIME Analytics platform and its application in bioinformatics (Webinar) https://tess.elixir-europe.org/events/knime-practical-introduction-to-knime-analytics-platform-and-its-application-in-bioinformatics-webinar This event introduces participants to the [KNIME](https://www.knime.com/) Analytics Platform, an open source data science platform with a visual workflow editor, that can be used by users without prior programming experience or integrated with existing scripts written in R or Python. These sessions are aimed towards anyone who has an interest in building data science workflows with different kinds of life science data. The sessions will cover how to aggregate data from different sources (e.g., files, databases, web services), how to calculate simple statistics (e.g., for data exploration), network mining (e.g., protein-protein interactions) and big data analytics (e.g., next-generation sequencing data). The webinar will combine practical and taught content to demonstrate how users can use KNIME to design and utilise reproducible data science workflows, such as analytics tasks, and better explore and understand their data. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3508000&amp;course-title=KNIME%20webinar).'' 2020-07-29 13:00:00 UTC 2020-07-30 15:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] This hands-on event is suitable for anyone who has an interest in building data science workflows with different kinds of life science data.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals<span style="color:#FF0000">There is no fee charged for this event''<span style="color:#FF0000"> workshops_and_courses [] HDRUK
  • Inferring Co-Expressing Genes and Regulatory Networks from RNA-Seq Data (Webinar)

    30 July 2020

    Cambridge, United Kingdom

    Elixir node event
    Inferring Co-Expressing Genes and Regulatory Networks from RNA-Seq Data (Webinar) https://tess.elixir-europe.org/events/inferring-co-expressing-genes-and-regulatory-networks-from-rna-seq-data-webinar One of the most important tasks of systems biology is to create explanatory and predictive models of complex biological systems. Availability of gene expression data in different conditions has paved the way for reconstructing direct or indirect regulatory connections between various genes and gene products. Most often, we are not interested in single interactions between gene products; instead, we try to reconstruct networks that provide insights into the investigated biological processes. This webinar will introduce the importance and applications of Gene Expression Datasets (Microarrays and RNA-Seq), followed by methods of extraction and analysis of Co-Expression Networks and Transcriptional Regulatory Networks from these datasets. The webinar will focus on the pros and cons of Weighted and Unweighted Networks, citing examples to aid decisions about which networks to use and when. The webinar will be presented in the form of a lecture and tutorial with screenshots that enable listeners to emulate the protocols in R. Note that this is a webinar and not a coding exercise. Links to further reading and practice will be shared. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3516387&amp;course-title=Co-Expressing%20Genes%20and%20Regulatory%20Networks%20webinar).'' 2020-07-30 10:00:00 UTC 2020-07-30 12:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] This webinar is suitable for students and early career researchers with interest in GenomicsGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals.<span style="color:#FF0000">There is no fee charged for this event''<span style="color:#FF0000">. workshops_and_courses [] HDRUK
  • Identification of Eigen-genes, consensus modules and Network Motifs in co-expression (or other biological) networks. (Webinar)

    10 August 2020

    Cambridge, United Kingdom

    Elixir node event
    Identification of Eigen-genes, consensus modules and Network Motifs in co-expression (or other biological) networks. (Webinar) https://tess.elixir-europe.org/events/identification-of-eigen-genes-consensus-modules-and-network-motifs-in-co-expression-or-other-biological-networks-webinar One of the most important tasks of systems biology is to create explanatory and predictive models of complex biological systems. Availability of gene expression data in different conditions has paved the way for reconstructing direct or indirect regulatory connections between various genes and gene products. Most often, we are not interested in single interactions between gene products; instead, we try to reconstruct networks that provide insights into the investigated biological processes or the entire system as a whole. This webinar will expand upon the concept of Gene Co-expression Networks to elucidate Weighted Gene Co-expression Network Analysis (WGCNA), and introduce the importance of visualising clustered gene expression profiles as single ‘Eigengenes’. It will describe the complete protocol for WGCNA analysis starting from normalised Gene Expression Datasets (Microarrays or RNA-Seq). This will be followed by a discussion on methods of extraction and analysis of consensus modules and Network motifs from Gene Co-Expression Networks and Transcriptional Regulatory Networks. The webinar will be presented in the form of a lecture and tutorial with screenshots that enable listeners to emulate the protocols in R. Note that this is a webinar and not a coding exercise. Links to further reading and practice will be shared. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3516410&amp;course-title=Identification%20of%20Eigen-genes%20in%20co-expression%20networks%20webinar).'' 2020-08-10 10:00:00 UTC 2020-08-10 12:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] This webinar is suitable for students and early career researchers with interest in GenomicsGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals.<span style="color:#FF0000">There is no fee charged for this event''<span style="color:#FF0000">. workshops_and_courses [] HDRUK
  • Using the Ensembl Genome Browser (ONLINE TRAINING)

    1 September 2020

    Cambridge, United Kingdom

    Elixir node event
    Using the Ensembl Genome Browser (ONLINE TRAINING) https://tess.elixir-europe.org/events/using-the-ensembl-genome-browser-467135ab-7028-4d4f-8a24-bbffa5548b3b PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. The [Ensembl Project](http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3351117&amp;course-title=Using%20the%20Ensembl%20Genome%20Browser).'' 2020-09-01 08:30:00 UTC 2020-09-01 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Gene transcripts Gene structure Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Ensembl REST API workshop (ONLINE TRAINING)

    2 September 2020

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API workshop (ONLINE TRAINING) https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-c3f269e2-c30f-4a2d-b719-a822af0359c5 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. The [Ensembl project](http://www.ensembl.org/) provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl [REST APIs](http://rest.ensembl.org/), including understanding the major endpoints and how to write scripts to call them. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3351102&amp;course-title=Ensembl%20REST%20API%20Workshop).'' 2020-09-02 08:30:00 UTC 2020-09-02 14:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Bioinformaticians and wet-lab biologists who can programGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Data Science School: Machine learning applications for life sciences

    21 - 24 September 2020

    Cambridge, United Kingdom

    Elixir node event
    Data Science School: Machine learning applications for life sciences https://tess.elixir-europe.org/events/data-science-school-machine-learning-applications-for-life-sciences This School aims to familiarise biomedical students and researchers with principles of Data Science. Focusing on utilising machine learning algorithms to handle biomedical data, it will cover: effects of experimental design, data readiness, pipeline implementations, machine learning in Python, and related statistics, as well as Gaussian Process models. Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application. This event is sponsored by [Cambridge Centre for Data-Driven Discovery (C2D3)](https://www.bigdata.cam.ac.uk/). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3357195&amp;course-title=Data%20Science%20School).'' 2020-09-21 09:00:00 UTC 2020-09-24 14:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Bioinformatics University of Cambridge Bioinformatics Training [] Students and researchers from life-sciences or biomedical backgroundswho haveor will shortly havethe need to apply the techniques presented during the course to biomedical data.The course is open to Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals<span style="color:#FF0000">Please note that all participants attending this course will be charged a registration fee. <span style="color:#0000FF"> Non-members of the University of Cambridge to pay £400. </span style> <span style="color:#0000FF">All Members of the University of Cambridge to pay £200. </span style> <span style="color:#FF0000">A booking will only be approved and confirmed once the fee has been paid in full.</span style> workshops_and_courses [] HDRUK
  • Computational genomics course for hands-on data analysis 2020

    23 - 25 September 2020

    Berlin, Germany

    Computational genomics course for hands-on data analysis 2020 https://tess.elixir-europe.org/events/computational-genomics-course-for-hands-on-data-analysis-2020 Educators: Altuna Alkalin, Verdan Franke, Bora Uyar (RBC/deNBI-epi Scientists from Berlin) Date: 15-17 June 2020 Location: BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin. Mitte Campus. Contents: The general aim of the course is to equip participants with practical and technical knowledge to analyze single cell RNA-seq data. With this aim in mind, we will go through unsupervised machine learning methods to analyze high-dimensional data sets, and move on to statistical methods developed to analyze bulk RNA-seq. Lastly, we will introduce analysis techniques used for single cell RNA-seq. There will be theoretical lectures followed by practical sessions where students directly apply what they have learned. The programming will be mainly done in R. Day 1: Intro to machine learning &amp; data visualization for genomics Day 2: Bulk RNA-seq analysis Day 3: Single cell RNA-seq analysis Learning goals: The course will be beneficial for first year computational biology PhD students, and experimental biologists and medical scientists who want to begin data analysis or are seeking a better understanding of computational genomics and analysis of popular sequencing methods.r Prerequisites: Some statistics and R programming experience will be good to keep up with the course. Practicals will be done in R. Keywords: Computational genomics, RNA-seq, Machine learing, Tools: R/Bioconductor Application Deadline: 15th of April 2020-09-23 09:00:00 UTC 2020-09-25 17:00:00 UTC de.NBI Berlin, Berlin, Germany Berlin Berlin Germany [] [] [] workshops_and_courses [] []
  • 3rd de.NBI Cloud Usermeeting

    8 - 14 October 2020

    3rd de.NBI Cloud Usermeeting https://tess.elixir-europe.org/events/3rd-de-nbi-cloud-usermeeting 3rd de.NBI Cloud Usermeeting Online Educators: de.NBI cloud group including Peter Belmann, Daniel Hübschmann, Peter Ebert, Martin Zurowietz, Kay Schallert, Sven Olaf Twardziok, Jan Krüger, Maximillian Hanussek, Martin Braun, Marius Dieckmann, Björn Grüning etc. Date: 8.10.2020 – 14.10.2020 Location: Online Contents: We are pleased to announce the third de.NBI Cloud User Meeting. In comparison to preceding meetings, this year`s meeting will be organized as an online conference. Over five days users can watch talks of already experienced users and long running projects and thereby learn about best practices in cloud computing. Same as the last years we will try to cover topics for beginners such as virtualization but also topics for software engineers and administrators such as orchestration with Kubernetes. Participants will learn how to scale up their analysis to handle growing input data and how to use workflow managers such as Snakemake in a cloud environment. As every year we are also going to demonstrate the usage of bioinformatics software in the de.NBI Cloud using Docker images or Bioconda packages. Planned Courses: - Running Snakemake Workflows in the de.NBI Cloud - OpenStack Introduction - BioConda and BioContainers - Kubernetes Introduction - Deploying Web Services in the de.NBI Cloud - Extensible Cluster Setup in the Cloud with BibiGrid and Ansible - Using Terraform to define infrastructure as code Learning goals: Working with the de.NBI cloud Prerequisites: We welcome people from all background, no matter if you are new to the de.NBI Cloud or considering to submit a project application, to learn and network in our growing community. Keywords: de.NBI cloud Tools: de.NBI cloud Webpage: https://cloud.denbi.de/3rd-de-nbi-cloud-user-meeting/ 2020-10-08 09:00:00 UTC 2020-10-14 17:00:00 UTC de.NBI [] [] [] meetings_and_conferences [] []

Note, this map only displays events that have geolocation information in TeSS.
For the complete list of events in TeSS, click the grid tab.