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DTSTAMP:20260715T221835Z
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DESCRIPTION:This course provides an introduction to the use of bioinformati
 cs in biological research\, giving participants guidance for using bioinfo
 rmatics in their work whilst also providing hands-on training in tools and
  resources appropriate to their research.\n\nParticipants will initially b
 e introduced to bioinformatics theory and practice\, including best practi
 ces for undertaking bioinformatics analysis\, data management\, and reprod
 ucibility. To enable specific exploration of resources in their particula
 r field of interest\, participants will then be divided into focused group
 s to work on a project.\n\nParticipants will be required to review some pr
 e-recorded material prior to the start of the course.\n\n### Group project
 s\n\nA major element of this course is a group project\, where participant
 s will be placed in small groups to work together on a challenge set by tr
 ainers from EMBL-EBI and external institutes. This allows people to explor
 e the bioinformatics tools and resources available in their area of intere
 st and apply them to a set problem\, providing participants with hands-on 
 experience relevant to their own research. The group work will culminate i
 n a presentation session involving all participants on the final day of th
 e course\, giving an opportunity for wider discussion on the benefits and 
 challenges of working with biological data.\n\nGroups are mentored and sup
 ported by the trainers who set the initial challenge\, but the groups will
  be responsible for driving their projects forward\, with all members expe
 cted to take an active role. Groups are pre-organised before the course\, 
 and all group members will be sent some short “homework” in preparatio
 n for their project work prior to the start of the course.\n\nBasic outlin
 es 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 wh
 ich you think would benefit your research most. Not all projects may be of
 fered\, and final decisions on which projects will be run during the cours
 e will be made based on the number of applicants per project.\n\nMost of t
 he projects cover mammalian data sets\, however\, in many cases\, the meth
 ods and approaches taught are transferable to data from various species.  
 \n  \n\n**Group project one | Genome variation across human populations 
 **\n\nNatural variation between individuals or between different human pop
 ulations is a result of genome mutations throughout evolutionary history. 
 Some mutations may become fixed because of their beneficial effect while m
 ost drift among individuals. During this project\, you will investigate ge
 nomic variation between two separate human populations of European and Asi
 an descent. Using sequence data from a number of individuals from each pop
 ulation\, you will use a range of bioinformatics tools to discover variant
 s that exist between them. In the second section of the project\, you will
  attempt to analyse the functional consequences of the variants you have i
 dentified\, attempting to find clinical association and linking them to ph
 enotypes.\n\nProject mentor: Baron Koylass | EMBL-EBI\n\n**Group project t
 wo | Interpreting functional information from large scale protein structur
 e data**\n\nThis project will introduce you to the wealth of publicly avai
 lable data in the [Protein Data Bank (PDB)](https://www.ebi.ac.uk/pdbe/) a
 nd give you the opportunity to investigate how large subsets of structure 
 data can be used to analyse protein features and determine function. In th
 e project\, you will learn how to: identify relevant protein structures\, 
 collate and interpret functional information\, and implement this process 
 programmatically.\n\nProject mentor: Preeti Choudhary | EMBL-EBI\; Marcus 
 Bage | EMBL-EBI  \n\n**Group project three | Modelling cell signalling p
 athways**\n\nCurating models of biological processes is an effective train
 ing in computational systems biology\, where the curators gain an integrat
 ive 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 softwar
 e such as COPASI even without extensive mathematical background. You will 
 learn to perform in-silico experiments\, new predictions\, and develop hyp
 otheses. Furthermore\, you will learn how to annotate models and re-use pr
 e-existing models from open repositories such as [BioModels](https://www.e
 bi.ac.uk/biomodels/).\n\nProject mentors: Rahuman Sheriff | EMBL-EBI\; Kri
 shna Tiwari | EMBL-EBI\n\n**Group project four | Networks and pathways**\n
 \nThis project will cover typical bioinformatics analysis steps needed to 
 put differentially expressed genes into a wider biological context. You wi
 ll start with gene expression data (RNA-seq) to build an initial interacti
 on network. Next\, you will learn to combine public network datasets\, ide
 ntify key regulators of biological pathways\, and explore biological funct
 ion through network analysis. You will get first-hand experience in integr
 ation and co-visualising with additional data and functional enrichment an
 alysis. All this helps to put the initial results into a previously known 
 context and provide hypotheses for potential follow up experiments. We wil
 l use Cytoscape\, [Expression Atlas](https://www.ebi.ac.uk/gxa/home)\, g:P
 rofiler\, StringDb\, among other tools. We also may give a few R packages 
 a try.\n\nProject mentor: Priit Adler | University of Tartu\n\n**Group pro
 ject five | Reusing FAIR Bioimage data: an AI application**\n\nBiological 
 imaging is a rapidly growing field with a vast potential of re-use for fur
 ther scientific research and development. Re-use of bioimage data requires
  FAIR (Findable\, Accessible\, Interoperable\, Reusable) data\, by public 
 repositories that support FAIR sharing\, such as the [BioImage Archive](ht
 tps://www.ebi.ac.uk/bioimage-archive/). This project aims to showcase one 
 of many ways of reusing bioimage data\, by applying artificial intelligenc
 e (AI) models on selected datasets in the [BioImage Archive](https://www.e
 bi.ac.uk/bioimage-archive/). In this project\, you will learn to search an
 d download the extensive variety of data that is held in this publicly ava
 ilable data resource. You will also use Jupyter Python notebooks to visual
 ise image data in the archive and deploy AI models on selected datasets.\n
 \nProject mentors: Aybuke Kupcu Yoldas | EMBL-EBI\; Teresa Zulueta-Coarasa
  | EMBL-EBI\n\n**Additional information**\n\nPlease note that we will oper
 ate this course face-to-face at EMBL-EBI in Hinxton. Hybrid options are no
 t currently available. We reserve the right to change the format of this c
 ourse or cancel it\, due to the ongoing coronavirus pandemic.
LOCATION:European Bioinformatics Institute\, Hinxton
SUMMARY:Summer school in bioinformatics
URL;VALUE=URI:https://www.ebi.ac.uk/training/events/summer-school-bioinform
 atics-0
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