5 events found
Differential Gene Expression Analysis with R (microarray and NGS)
25 May 2016
Brisbane, AustraliaDifferential Gene Expression Analysis with R (microarray and NGS) http://www.qfab.org/event/workshop-analysis-of-microarray-and-ngs-data-with-r-2-2/ https://tess.elixir-europe.org/events/differential-gene-expression-analysis-with-r-microarray-and-ngs This hands-on workshop will introduce users of the R software environment to the specific skills and applications used in the analysis of microarray and next-generation sequencing (NGS) data. Practical exercises will include quality control and normalisation of data for differential gene expression, and linking genomic information to external public datasets. Recommended participants Biologists and bioinformaticians wishing to use R for RNA expression analysis. Prior expertise with R and the command line interface is required, to a level equivalent of that provided by the QFAB workshop “Introduction to R”. What will I learn? During this course you will learn about: Pre-processing and quality control of microarray and RNA-Seq data The use of R packages for the identification of differentially-expressed genes from expression data Systems biology interpretation of gene lists using pathway analysis Integration of expression and genome data with Ensembl databases After this course you should be able to: Import Affymetrix CEL files to R as data objects Carry out standard QC tests on microarray and RNA-Seq datasets Use the limma-voom R package to produce lists of differentially expressed genes between pairs of samples Identify over-represented gene ontology categories in gene lists using the GOStats package 2016-05-25 09:00:00 UTC 2016-05-25 00:00:00 UTC University of Queensland, Brisbane, Australia University of Queensland Brisbane Australia Sequencing Gene expression Data architecture, analysis and design    workshops_and_courses  ABRQFABR
Software Carpentry with R COMBINE Workshop
11 - 12 July 2016
Brisbane, AustraliaSoftware Carpentry with R COMBINE Workshop http://www.eventbrite.com.au/e/software-carpentry-with-r-uq-winter-school-workshop-tickets-22386171642 https://tess.elixir-europe.org/events/software-carpentry-with-r-combine-workshop This Software Carpentry with R workshop is a tie-in to the 2016 UQ Winter School in Mathematical and Computational Biology. The workshop is being brought to you by COMBINE. Attendees must have registered for at least some part of the UQ Winter School. 2016-07-11 09:00:00 UTC 2016-07-12 00:00:00 UTC University of Queensland Brisbane, Australia Brisbane Australia Data architecture, analysis and design Computer science Bioinformatics    workshops_and_courses  ABRCOMBINEBioinformatics
ELIXIR-EXCELERATE HPC Train-the-Researcher
6 - 7 April 2017
Málaga, SpainELIXIR-EXCELERATE HPC Train-the-Researcher https://chirimoyo.ac.uma.es/bitlab/portfolio/hpc-excelerate/#course-info https://tess.elixir-europe.org/events/elixir-excelerate-hpc-train-the-researcher This course to be held 6-7 April 2017 in Malaga, Spain is part of the Train-the-Researcher (TtR) subtask of the ELIXIR-EXCELERATE project. The course is organised as a two-day mini-symposium, and aims at introducing the participants in the complexities of parallel programming with emphasis on genome-scale comparison algorithms. The theoretical aspects of this course cover (a) the parallel programing background, with a quick overview in the architectures and programming models; and (b) the basis for genome-scale sequence comparison algorithms. The practical aspects are organised to master the concepts of data distribution and balancing using a Map-Reduce strategy and internal coding with MPI. Organization Overview This course has been prepared for two days including theoretical and practical parts. The first day will start with a brief introduction to HPC condensed during the morning. A practical introductory part to HPC will complete the first day. The second day will firstly provide the necessary background on the multiple genome comparison application GECKO. Secondly, on the same day, we will motivate the potential HPC techniques to be applied to this application and will let the students organize in groups to start thinking about a parallelization approach and later on implementing it. At the end of the day each group will briefly describe how they have implemented it and will present their results (i.e. speedup). Methods The course is comprised of practical exercises preceded by short lectures. Exercises will be conducted primarily in the C programming language using the MPI library. Target Audience This course is open to bioinformatics users and developers that aim at using HPC resources to extend their activity beyond the limitations of sequential applications on commodity hardware. This course will not suit participants that are looking for entry-level concepts in HPC. 20 participants will be selected by CV and motivation. Gender equality will be an additional aspect to select the participants. As an applicant to this course you need to fill out your personal information, attach your CV and provide a short paragraph to explain why you want to apply for this course. Optionally if you are part of an ELIXIR node you can also attach a letter of endorsement from the node manager. The last application day will be March 3rd, the result of the candidate selection will be notified March 8th. The course registration is free, but by sending this participation you commit to attend the course in case you are selected as it is stated in the conditions/policy document of the registration form. Pre-Requisites This course has a broad technical scope and hence programming skills are required. Experience in the command-line, writing and compiling C code would make the course easier to follow. 2017-04-06 09:00:00 UTC 2017-04-07 17:00:00 UTC Málaga, Málaga, Spain Málaga Málaga Málaga Spain Sequence analysis Computer science   software developers, bioinformaticians workshops_and_courses registration_of_interest 
ELIXIR-EXCELERATE HPC Train-the-Researcher course
6 - 7 April 2017
Málaga, SpainELIXIR-EXCELERATE HPC Train-the-Researcher course https://elixir.mf.uni-lj.si/course/view.php?id=21 https://tess.elixir-europe.org/events/elixir-excelerate-hpc-train-the-researcher-course-3af9b3c7-94a5-46ae-a68c-1c73b87049ab ELIXIR-EXCELERATE HPC Train-the-Researcher course, Apr 6-7, 2017, Malaga, Spain 2017-04-06 09:00:00 UTC 2017-04-07 17:00:00 UTC Escuela Técnica Superior de Ingeniería Informática Escuela Técnica Superior de Ingeniería Informática, 35, Bulevar Louis Pasteur, Málaga, Spain Escuela Técnica Superior de Ingeniería Informática, 35, Bulevar Louis Pasteur Málaga Málaga Spain Computational biology Computer science Escuela Técnica Superior de Ingeniería Informática, University of Malaga  life scientistsResearchers workshops_and_courses registration_of_interest high-performance computingtrainingeLearningEeLP
Advances in Computational Biology Conference 2019
28 - 29 November 2019
Barcelona, SpainAdvances in Computational Biology Conference 2019 https://www.iscb.org/advcompbio2019 https://tess.elixir-europe.org/events/advances-in-computational-biology-conference-2019 The first **Advances in Computational Biology conference – _Fostering collaboration among women scientists_** will bring together researchers working on systems biology, omics technologies, artificial intelligence and high-performance computing with applications to biology from both the public and private sectors. One of the main purposes of the conference is to **visualize and promote the research done by women scientists** and for this reason, all presenters will be women, although the conference is open to everyone. We want to create a space to foster collaborations between scientists, providing an excellent opportunity to share ideas and build research networks. Topics included: - **Learning from Biological Sequences**: population genomics, evolutionary genomics, systems biology, transcriptomics, sequence analysis - **When Computational Biology meets Medicine**: biomedical applications, mutational landscapes, clinical genomics - **Machines Speeding up Research**: high performance computing, machine learning in the life sciences, imaging data analysis, dynamic simulations and algorithm development Key dates: - Open registration: May 6th, 2019 - Abstract submission opens: May 6th, 2019 - **Abstract submission deadline: July 1st, 2019** - Early bird registration deadline: September 15th, 2019 - Registration deadline: November 1st, 2019 - AdvCompBio Conference: November 28th - 29th, 2019 The programme will include poster and oral presentations, as well as keynotes from leading scientists in the computational biology and high-performance computing fields. The keynote speakers of the conference are: **Christine Orengo**, group leader of Orengo Group at University College London, **Natasa Przulj**, group leader of the Life Sciences – Integrative Computational Network Biology at the Barcelona Supercomputing Center and **Marie-Christine Sawley**, director of the Exascale Lab at Intel. The confirmed chairs of the conference are: **Alison Kennedy**, director of the STFC Hartree Centre, **Janet Kelso**, group leader of the Minerva Research Group for Bioinformatics at the Max Planck Institute for Evolutionary Anthropology, and **Nuria Lopez-Bigas**, leader of the Biomedical Genomics Research Group at the Institute for Research in Biomedicine Barcelona. Furthermore, the participants will have the opportunity to interact personally with female leaders in the fields of IT, academic research and politics that support the conference. The conference is organised by the Bioinfo4Women programme from the Barcelona Supercomputing Center (BSC-CNS) with the collaboration of IMIM-UPF Research Programme on Biomedical Informatics (GRIB), the Spanish National Bioinformatics Institute (INB/ELIXIR-ES) and the Universitat Politècnica de Catalunya (UPC). It is an affiliate conference of the International Society for Computational Biology (ISCB). 2019-11-28 09:00:00 UTC 2019-11-29 17:00:00 UTC La Pedrera, 92, Passeig de Gràcia, Barcelona, Spain La Pedrera, 92, Passeig de Gràcia Barcelona Barcelona Spain Imaging Machine learning Computational biology Computer science Biomedical science Sequence analysis Transcriptomics Evolutionary biology Population genomics Omics Systems biology Bioinformatics   ResearchersPhD studentsPostdoctoral studentsComputer scienceComputational biologistsbioinformaticians meetings_and_conferences  HPCBioinformaticsComputational BiologyArtificial IntelligenceGenomicsTranscriptomicsSystems biologyPopulation GenomicsEvolutinary genomicsSequence Analysisbiomedical applicationsmutational landscapesclinical genomicsImagingdynamic simulationsalgorithmsmachine learning
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