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22 events found

Country: Portugal  or United Kingdom  or Belgium 

  • "Ready for BioData Management?" Data Stewardship program for the life sciences

    21 February - 31 October 2022

    Oeiras, Portugal

    "Ready for BioData Management?" Data Stewardship program for the life sciences https://tess.elixir-europe.org/events/ready-for-biodata-management-data-stewardship-program-for-the-life-sciences BioData.pt | ELIXIR Portugal, in collaboration with several other organizations has designed a program to train the first generation of Data Stewards for the life sciences, to support the implementation of data management, open science and FAIR data principles in Portuguese R&I organizations. It will unfold from February to October 2022, allowing trainees get some practice and consolidate the acquired knowledge. It will comprise an introductory module covering the basic concepts of Data Stewardship followed by two assignments and end with a hands-on course for knowledge consolidation. 2022-02-21 09:00:00 UTC 2022-10-31 17:00:00 UTC BioData.pt | ELIXIR Portugal Online and F2F (See details in training documentation), Oeiras, Portugal Online and F2F (See details in training documentation) Oeiras Portugal FAIR data Data submission, annotation, and curation Bioinformatics Data management Biodata.pt - Elixir's portuguese node of the european projec info@biodata.pt ELIXIR Life Science Researchers 24 workshops_and_courses registration_of_interest data managementData management plandata stewardshipdata annotationlife sciencestraining
  • Developing ELIXIR's Future Programme

    6 June 2022

    Belgium

    Developing ELIXIR's Future Programme https://tess.elixir-europe.org/events/developing-elixir-s-future-programme ELIXIR is currently developing it’s Scientific Programme for 2024-2028. Over the last year we have had a number of working groups looking at life-science data challenges and how we think ELIXIR can support data intensive research. But we also want to have a open, pubic debate about opportunities, challenges and priorities for the European life-science data infrastructure. We are therefore organising a high-level workshop in Brussels and invite senior representatives from different research communities to give their perspective on the future.  We foresee a format with a series of short presentations (10 minutes) from our high-level panelists that will give inspiration to round-table discussions between the all the workshop participants - each table will then make some recommendations at the end of the debate.  2022-06-06 08:30:00 UTC 2022-06-06 08:30:00 UTC Belgium Belgium [] [] [] [] [] []
  • Bioinformatics for principal investigators

    8 - 10 June 2022

    United Kingdom

    Elixir node event
    Bioinformatics for principal investigators https://tess.elixir-europe.org/events/bioinformatics-for-principal-investigators-65ee8139-bbbe-4fb3-9a29-ee2dcd36456f This course has been designed to provide Principal Investigators (PI's) working in the life sciences with an introduction to the challenges of working with biological data as a research leader. Starting with a look at where bioinformatics and data science fits into their research teams, the course will enable PI’s to take a strategic look at the requirements for undertaking such work and how bioinformatics capacity can be developed from personnel through to computational needs.  It will additionally provide guidance on strategies for managing data, and the importance of data sharing; how to work with computational collaborators and what resources are available across the life sciences to support such work. During this course we will not be teaching hands-on bioinformatics analysis, but we will be signposting appropriate training resources to upskill you and your team. This course is organised in parallel with Managing a Bioinformatics Core Facility to maximise opportunities for networking. Shared sessions are highlighted in bold in the course programme. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing. 2022-06-08 09:00:00 UTC 2022-06-10 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] This course is aimed at both new and established investigators who lead a research team which currently uses bioinformatics, or where bioinformatics will be a component in future research. No prior knowledge of bioinformatics, or experience of analysis is required for this course. Applications are invited from investigators working in all settings, including academic, clinical, and industrial organisations. 20 [] [] []
  • Managing a bioinformatics core facility

    8 - 10 June 2022

    United Kingdom

    Elixir node event
    Managing a bioinformatics core facility https://tess.elixir-europe.org/events/managing-a-bioinformatics-core-facility-9f586926-41df-4736-ae50-9ccbdbabaab8 This knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL-EBI’s service teams, from each other, and from potential users of their services. These facilities play an essential role in enabling research in the molecular life sciences. The landscape is constantly evolving as new research tools emerge, as experiments become increasingly data intensive, and as their clients – experimental researchers – become more exposed to the power of data-driven biology. This course will allow participants to share experiences, discuss challenges and solutions that they face, and plan ways to cope with the ever changing demands raised by the molecular life science field. It will include sessions to learn from data providers at EMBL-EBI, hear how others have tackled common problems, and work together to design core services. This course is organised in parallel with Bioinformatics for principal investigators to maximise opportunities for networking. Shared sessions are highlighted in bold in the course programme. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing. 2022-06-08 09:00:00 UTC 2022-06-10 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] This workshop is aimed at new and experienced managers of bioinformatics core facilities, or other facilities that support their users to analyse and interpret large biomolecular data sets.  This course will not provide a platform for teaching hands-on bioinformatics analysis.   15 [] [] []
  • Summer school in bioinformatics

    13 - 17 June 2022

    United Kingdom

    Elixir node event
    Summer school in bioinformatics https://tess.elixir-europe.org/events/summer-school-in-bioinformatics-f81334cb-06e3-4263-bfd0-74c9c542615b This course, organised in association with Wellcome Connecting Science, provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research. Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management, and reproducibility. To enable specific exploration of resources in their particular field of interest, participants will be divided into focused groups to work on a project set by resource and data experts from EMBL-EBI and external collaborating institutes. These projects will end with a presentation from each group on the final day of the course to bring together learnings from all participants. Participants will be required to review some pre-recorded material prior to the start of the course and will have an opportunity to meet other trainees in an induction session to be held virtually in the week before the course take place. Group projects A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI and external institutes. This allows people to explore the bioinformatics tools and resources available in their area of interest and apply them to a set problem, providing participants with hands-on experience relevant to their own research. The group work will culminate in a presentation session involving all participants on the final day of the course, giving an opportunity for wider discussion on the benefits and challenges of working with biological data. Groups are mentored and supported by the trainers who set the initial challenge, but the groups will be responsible for driving their projects forward, with all members expected to take an active role. Groups are pre-organised before the course, and all group members will be sent some short “homework” in preparation for their project work prior to the start of the course. Basic outlines of the projects on offer this year are given below. In your application you must indicate your first and second choice of project, based on which you think would benefit your research most. Not all projects may be offered, and final decisions on which projects will be run during the course will be made based on the number of applicants per project. Most of the projects cover mammalian data sets, however, in many cases, the methods and approaches taught are transferable to data from various species. Networks and pathways This project will cover typical bioinformatics analysis steps needed to put differentially expressed genes into a wider biological context. You will start with gene expression data (RNA-seq) to build an initial interaction network. Next, you will learn to combine public network datasets, identify key regulators of biological pathways, and explore biological function through network analysis. You will get first-hand experience in integration and co-visualising with additional data and functional enrichment analysis. All this helps to put the initial results into a previously known context and provide hypotheses for potential follow up experiments. We will use Cytoscape, Expression Atlas, g:Profiler, StringDb, among other tools. We also may give a few R packages a try. Project mentors: Priit Adler (University of Tartu), Hedi Peterson (University of Tartu) Genome variation across human populations Natural variation between individuals or between different human populations is a result of genome mutations throughout evolutionary history. Some mutations may become fixed because of their beneficial effect while most drift among individuals. During this project, you will investigate genomic variation between two separate human populations of European and Asian descent. Using sequence data from a number of individuals from each population, you will use a range of bioinformatics tools to discover variants that exist between them. In the second section of the project, you will attempt to analyse the functional consequences of the variants you have identified, linking them to phenotypes. Project mentors: Baron Koylass (EMBL-EBI) Modelling cell signalling pathways Curating models of biological processes is an effective training in computational systems biology, where the curators gain an integrative knowledge of biological systems, modelling, and bioinformatics. You will learn to encode and simulate ordinary differential equation models of signalling pathways from a recent publication using user-friendly software such as COPASI even without extensive mathematical background. You will learn to perform in-silico experiments, new predictions, and develop hypotheses. Furthermore, you will learn how to annotate models and re-use pre-existing models from open repositories such as BioModels. Project mentors: Rahuman Sheriff (EMBL-EBI)  Interpreting functional information from large scale protein structure data This project will introduce you to the wealth of publicly available data in the Protein Data Bank (PDB) and give you the opportunity to investigate how large subsets of structure data can be used to analyse protein features and determine function. In the project you will learn how to: identify relevant protein structures, collate and interpret functional information, and implement this process programmatically. Project mentors: David Armstrong (EMBL-EBI), Preeti Choudhary (EMBL-EBI) Analysis of intercellular interactions in healthy and diseased states Ulcerative colitis is an inflammatory bowel disease. The exact pathomechanism of the disease is unknown. However, the interactions between the intestinal immune cells and the intestinal epithelial cells play a crucial role during the development of the disease. Single-cell RNA-seq measurements can help us understand these complex interactions. The expression data combined with protein-protein interaction databases can shed light on the connections between cells in diseased and healthy states. During this project, you will use a single-cell RNA-seq dataset to build interactions between the various cells. The dataset contains pre-processed, cell type classified data of biopsies from healthy, inflamed and non-inflamed UC colonic biopsies. The interactions between cells will be downloaded from the OmniPath database. You will use Python Notebooks to build up the intercellular networks, map the single cell RNA-seq expression data and visualise them. The intercellular networks between various cell types can then be compared by Cytoscape. Project mentors: Dezso Modos (Quandram Institute Bioscience), Marton Olbei (Earlham Institute) 2022-06-13 09:00:00 UTC 2022-06-17 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their knowledge and skills further. No previous knowledge of programming is required for this course; group projects may give you the opportunity to learn basic programming, but participants will be supported in this by their mentors. Depending on your chosen project, an introductory programming tutorial may be given as homework prior to attending the course. Though programming skills are not a prerequisite for attending the course, we will ask participants to specify their current level of programming skills in the applications. This will allow the mentors to target the group projects better to the skills and needs of the final course participants. 30 [] [] Protein Data Bank in Europe BioModels database European Nucleotide Archive Ensembl Cross domain (cross-domain)
  • Introduction to RNA-seq analysis in R

    13 - 17 June 2022

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-bf632692-0913-4873-aef1-bac9a7c33e6b In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the DESeq2 analysis workflow. You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps. This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available.. 2022-06-13 11:30:00 UTC 2022-06-17 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to R for Biologists (ONLINE LIVE TRAINING)

    15 - 23 June 2022

    Cambridge, United Kingdom

    Elixir node event
    Introduction to R for Biologists (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/introduction-to-r-for-biologists-online-live-training-c59887f9-3eb5-49fd-a124-dee8194ac81a R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4178900&course-title=Introduction%20to%20R%20for%20Biologists).'' 2022-06-15 08:30:00 UTC 2022-06-23 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 [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Analysis of single cell RNA-seq data (ONLINE LIVE TRAINING)

    17 June - 1 July 2022

    Cambridge, United Kingdom

    Elixir node event
    Analysis of single cell RNA-seq data (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/analysis-of-single-cell-rna-seq-data-online-live-training-b8ef1f2a-776d-42f4-a490-f018700ae7ba Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging. In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4306409&&course-title=Analysis%20of%20single%20cell%20RNA-seq%20data).'' 2022-06-17 08:30:00 UTC 2022-07-01 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Transcriptomics Functional genomics Data visualisation Data mining 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
  • EMBL-EBI: Network Analysis with Cytoscape (Online)

    20 - 21 June 2022

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Network Analysis with Cytoscape (Online) https://tess.elixir-europe.org/events/embl-ebi-network-analysis-with-cytoscape-online-b82c9960-d4ec-4b28-bd6c-c6e413c587cf This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of one of the most commonly used open source Network Visualisation Platforms, [Cytoscape](https://cytoscape.org/what_is_cytoscape.html). The course will also access and analyse the data through Cytoscape apps, including IntAct app. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4306738&course-title=EMBL-EBI:%20Network%20Analysis%20with%20Cytoscape).'' 2022-06-20 08:30:00 UTC 2022-06-21 12:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] This workshop is aimed at researchers interested in proteinsnetwork analysisprotein-protein interactions and related areasBiologists and bioinformaticiansGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Reproducible Research with R (ONLINE LIVE TRAINING)

    20 June 2022

    Cambridge, United Kingdom

    Elixir node event
    Reproducible Research with R (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/reproducible-research-with-r-online-live-training-f5c6b5ba-52df-4afd-b3fb-c828d022d030 This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4283511&course-title=Reproducible%20Research%20with%20R).'' 2022-06-20 08:30:00 UTC 2022-06-20 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
  • Cancer genomics

    20 - 24 June 2022

    United Kingdom

    Elixir node event
    Cancer genomics https://tess.elixir-europe.org/events/cancer-genomics-7e5000fc-53f2-4282-bc4e-e16a5e7c22ab This course will focus on the analysis of data from genomic studies of cancer.  Talks and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data, whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the trainers. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing. 2022-06-20 09:00:00 UTC 2022-06-24 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] This course is aimed at PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies in cancer research and wish to familiarise themselves with bioinformatics tools and data analysis methodologies specific to cancer data. Familiarity with the technology and biological use cases of high throughput sequencing (HTS) is required, as is some experience with R/Bioconductor (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system. 30 [] [] []
  • Core Statistics using R (ONLINE LIVE TRAINING)

    29 June - 14 July 2022

    Cambridge, United Kingdom

    Elixir node event
    Core Statistics using R (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/core-statistics-using-r-online-live-training-1bdf4c7a-2283-4160-b3e3-4a8e7385502d This [award winning](https://www.cctl.cam.ac.uk/teaching-prizes/tel-prize/2020) virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course: # Use R confidently for statistics and data analysis # Be able to analyse datasets using standard statistical techniques # Know which tests are and are not appropriate R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4180988&course-title=Core%20Statistics%20using%20R).'' 2022-06-29 08:30:00 UTC 2022-07-14 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 [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individualsThis course is included as part of several DTP and MPhil programmesas well as other departmental training within the University of Cambridge (potentially under a different name) so participants who have attended statistics training elsewhere should check before applying. workshops_and_courses [] HDRUK
  • Building Workflows in Digital Health

    29 June 2022

    Manchester, United Kingdom

    Building Workflows in Digital Health https://tess.elixir-europe.org/events/building-workflows-in-digital-health Orchestration Workflows are widely used in computational data analysis, enabling innovation and decision-making. Often the analysis components are numerous, and written by third parties, without an eye on interoperability. In addition, many competing workflow systems exist, potentially limiting portability of workflows written for any one specific workflow system. This hinders the transfer of workflows between different systems and projects, limiting their re-usability. The Common Workflow Language (CWL) project (https://www.commonwl.org/) was established in order to produce free and open standards for describing command-line tool-based workflows. The CWL language is declarative and provides a focused set of common abstractions enabling the expression of computational workflows constructed from diverse software tools. Explicit declaration of requirements for runtime environments and software containers enables portability and reuse. Workflows written according to the CWL standards are a reusable description of that analysis, runnable on a diverse set of computing environments. 2022-06-29 10:00:00 UTC 2022-06-29 17:00:00 UTC N8CIR University Place, University of Manchester, Manchester, United Kingdom University Place, University of Manchester Manchester United Kingdom M13 9PL Bioinformatics Workflows Data architecture, analysis and design University of Manchester [] [] workshops_and_courses registration_of_interest workflowsdata-analysiscomputational methods
  • Systems biology: from large datasets to biological insight

    4 - 8 July 2022

    United Kingdom

    Elixir node event
    Systems biology: from large datasets to biological insight https://tess.elixir-europe.org/events/systems-biology-from-large-datasets-to-biological-insight-d2a1656c-29ef-412d-9ddb-233bf139d811 This course covers the use of computational tools to extract biological insight from omics datasets. The content will explore a range of approaches - ranging from network inference and data integration to machine learning and logic modelling - that can be used to extract biological insights from varied data types. Together these techniques will provide participants with a useful toolkit for designing new strategies to extract relevant information and understanding from large-scale biological data. The motivation for running this course is a result of advances in computer science and high-performance computing that have led to groundbreaking developments in systems biology model inference. With the comparable increase of publicly-available, large-scale biological data, the challenge now lies in interpreting them in a biologically valuable manner. Likewise, machine learning approaches are making a significant impact in our analysis of large omics datasets and the extraction of useful biological knowledge. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing. 2022-07-04 09:00:00 UTC 2022-07-08 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] This course is aimed at advanced PhD students, post-doctoral researchers, and non-academic scientists who are currently working with large-scale omics datasets with the aim of discerning biological function and processes. Ideal applicants should already have some experience (ideally 1-2 years) working with systems biology or related large-scale (multi-)omics data analyses. Applicants are expected to have a working knowledge of the Linux operating system and the ability to use the command line. Experience of using a programming language (i.e. Python) is highly desirable, and while the course will make use of simple coding or streamlined approaches such as Python notebooks, higher levels of competency will allow participants to focus on the scientific methodologies rather than the practical aspects of coding and how they can be applied in their own research. We recommend these free tutorials: Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training Python tutorial: https://www.w3schools.com/python/ R tutorial: https://www.datacamp.com/courses/free-introduction-to-r Regardless of your current knowledge we encourage successful participants to use these to prepare for attending the course and future work in this area. Selected participants will also be sent materials prior to the course. These might include pre-recorded talks and required reading that will be essential to fully understand the course. 30 [] [] []
  • Introduction to working with UNIX and bash (ONLINE LIVE TRAINING)

    6 - 7 July 2022

    Cambridge, United Kingdom

    Elixir node event
    Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/introduction-to-working-with-unix-and-bash-online-live-training-b013c4ea-fc73-42d1-9ac5-b11435801e1b PLEASE NOTE The Bioinformatics Team are presently teaching many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands. Building on the techniques learnt so far, we will then construct bash scripts combining the commands and structures already learnt into more complex, reusable tools. We will look at how we can apply these scripts to common problems faced in UNIX environments such as: communicating with remote servers; managing custom software installations and integrating these tools into our simple pipelines. This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4316938&course-title=Introduction%20to%20working%20with%20Unix%20and%20bash).'' 2022-07-06 13:00:00 UTC 2022-07-07 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
  • Bioinformatics for T-Cell immunology

    11 - 15 July 2022

    United Kingdom

    Elixir node event
    Bioinformatics for T-Cell immunology https://tess.elixir-europe.org/events/bioinformatics-for-t-cell-immunology This course will introduce and explore a number of key bioinformatics tools and resources that can be applied to T-cell immunological research. Targeted at life scientists with a wet-lab focus, it will provide participants with an overview of best-practice methods in applying bioinformatics approaches and enable them to become confident users of their own and public domain data. The resources introduced during the course will cover a variety of data types, from genomic data to computational models, and biological pathways. Participants will gain experience of the analysis pipelines for RNA-Seq and flow cytometry experiments as well as data integration of -omics data and basics concepts of machine learning approaches.This course has been developed in collaboration with the ENLIGHT-TEN+ project, a consortium focused on developing early-stage research expertise in T-cell immunology and big data analysis. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing. 2022-07-11 09:00:00 UTC 2022-07-15 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] The course is aimed at wet-lab scientists working in the field of immunology who wish to learn more about available data and tools that can help them in their research. 15 places are reserved for early-stage researchers from the ENLIGHT-TEN+ project.   30 [] [] []
  • High Performance Computing: An Introduction (ONLINE LIVE TRAINING)

    13 - 14 July 2022

    Cambridge, United Kingdom

    Elixir node event
    High Performance Computing: An Introduction (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/high-performance-computing-an-introduction-online-live-training-2e94ddaf-6071-4664-9d5d-619b49b20888 PLEASE NOTE The Bioinformatics Team are presently teaching many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Have you heard about High Performance Computing, but are not sure what it is or whether it is relevant for your work? Would you like to use a HPC, but are not sure where to start? Are you using your personal computer to run computationally demanding tasks, which take long and slow down your work? Do you need to use software that runs on Linux, but don't have access to a Linux computer? If any of these questions apply to you, then this course might be for you! Knowing how to work on a High Performance Computing system is an essential skill for applications such as bioinformatics, big-data analysis, image processing, machine learning, parallelising tasks, and other high-throughput applications. In this course we will cover the basics of High Performance Computing, what it is and how you can use it in practice. This is a hands-on workshop, which should be accessible to researchers from a range of backgrounds and offering several opportunities to practice the skills we learn along the way. As an optional session for those interested, we will also introduce the (free) HPC facilities available at Cambridge University (the course is not otherwise Cambridge-specific). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4316957&course-title=High%20Performance%20Computing:%20An%20Introduction).'' 2022-07-13 13:00:00 UTC 2022-07-14 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 [] This course is aimed at students and researchers of any background.We assume no prior knowledge of what a HPC is or how to use it.It may be particularly useful for those who have attended other Facility Courses and now need to process their data on a Linux server. It will also benefit those who find themselves using their personal computers to run computationally demanding analysis/simulations and would like to learn how to adapt these to run on a HPC.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Proteomics bioinformatics

    17 - 22 July 2022

    United Kingdom

    Elixir node event
    Proteomics bioinformatics https://tess.elixir-europe.org/events/proteomics-bioinformatics-e45e1bf8-c758-491b-817d-e236414eb179 This course provides hands-on training in the basics of mass spectrometry (MS) and proteomics bioinformatics, search engines and post-processing software, quantitative approaches, MS data repositories, the use of public databases for protein analysis, annotation of subsequent protein lists, and incorporation of information from molecular interaction and pathway databases. This course is organised in association with the Vlaams Instituut voor Biotechnologie (VIB). In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing. 2022-07-17 09:00:00 UTC 2022-07-22 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] The course is aimed at research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff, as well as specialists in related fields. The practical elements of the course will take raw data from a proteomics experiment and analyse it. Participants will be able to go from MS spectra to identifying and quantifying peptides, and finally to obtaining lists of protein identifiers that can be analysed further using a wide range of resources. The final aim is to provide attendees with the practical bioinformatics knowledge they need to go back to the lab and process their own data when collected. 30 [] [] []
  • Mathematics of life: modelling molecular mechanisms

    12 - 16 September 2022

    United Kingdom

    Elixir node event
    Mathematics of life: modelling molecular mechanisms https://tess.elixir-europe.org/events/mathematics-of-life-modelling-molecular-mechanisms-1b57c504-4751-4313-a48d-3ac2da24ab02 This course will provide participants with an introduction and hands-on training on modelling approaches, tools and resources used in systems biology as well as touch on network analysis. Computer models are increasingly used to understand the essential processes of biology. Researchers in academic institutions as well as the pharmaceutical industry use mathematical models to generate hypotheses on how complex biomolecular systems work. Modelling of biochemical pathways deregulated in disease conditions can offer mechanistic insights into the pathology, help to elucidate mechanisms behind drug action, and predict the dose required for treatment thus facilitating fundamental research and drug discovery. This course will provide a helpful brief introduction to key modelling concepts and hands on training to use popular tools and resources used in this scientific field. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing. 2022-09-12 09:00:00 UTC 2022-09-16 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] This course is aimed at experimental biologists, bioinformaticians and mathematicians who have just started in systems biology, are familiar with the basic terminology in this field and who are now keen on gaining a better knowledge of systems biology modelling approaches to understand biological and biomedical problems. An experience of using a programming language (e.g Python, R, Matlab) would be a benefit but is not mandatory. An undergraduate knowledge of molecular and cellular biology or some background in mathematics is highly beneficial. 30 [] [] []
  • Bioinformatics and functional genomics in zebrafish

    26 - 30 September 2022

    United Kingdom

    Elixir node event
    Bioinformatics and functional genomics in zebrafish https://tess.elixir-europe.org/events/bioinformatics-and-functional-genomics-in-zebrafish Zebrafish are widely used to study development, toxicity and disease, and functional genomics is used throughout the field to identify new pathways and mechanisms and for comparison to other model systems and humans. In this hands-on course, participants will learn how to design functional genomics experiments, manage and analyse RNA-seq datasets from zebrafish, and compare results to other species. The aim of the course is to equip researchers with tools to carry out functional analysis and data visualisation of RNA-seq data that has already been mapped to the genome and been analysed for differential gene expression. The course will be relevant to researchers working on a wide range of topics and will use real datasets from our lab for hands-on analysis. Who is this course for? This course is aimed at researchers currently working with zebrafish and generating genomic and functional data. Graduate students, postdoctoral fellows, research scientists and faculty are encouraged to apply.  Little to no experience with RNA-seq analysis is required, however, applicants who have already generated an RNA-seq dataset from zebrafish samples relevant to their project will gain the most benefit from this course.  Some experience with R is beneficial. Please note this information is from the 2019 course edition and may change slightly for the course taking place in 2022.  2022-09-26 09:00:00 UTC 2022-09-30 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] [] 30 [] [] []
  • Single-cell RNA-seq analysis using R

    3 - 7 October 2022

    United Kingdom

    Elixir node event
    Single-cell RNA-seq analysis using R https://tess.elixir-europe.org/events/single-cell-rna-seq-analysis-using-r-b67492cf-c2ef-4d84-abf9-f33d9626cd86 This course covers the analysis of scRNA-seq data using R and command line tools. Participants will be guided through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. They will explore and interpret data using R as well as the Single Cell Expression Atlas. Finally participants will put their knowledge into practice through a group challenge on the last two days of the course. Please note that participants will not analyse their own data as part of the course. There will, however, be ample opportunity to discuss their research and ideas with other course participants and trainers. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.  Full programme details will be added in due course.   2022-10-03 09:00:00 UTC 2022-10-07 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] [] 30 [] [] []
  • Structural bioinformatics

    17 - 21 October 2022

    United Kingdom

    Elixir node event
    Structural bioinformatics https://tess.elixir-europe.org/events/structural-bioinformatics-f94b8ddd-31e6-4539-b4c9-fdff8bc0b841 Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page.  We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest. 2022-10-17 09:00:00 UTC 2022-10-21 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] [] 30 [] [] []

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