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Content provider: Birmingham Metabolomics Tra...  or NBIS  or ELIXIR Portugal 

  • PDA17 Proteomics Data Analysis

    6 March 2017

    Oeiras, Portugal

    Elixir node event
    PDA17 Proteomics Data Analysis https://tess.elixir-europe.org/events/proteomics-data-analysis    IMPORTANT DATES for this Course   Deadline for applications: Feb 25th 2017 (New)   Course date: March 6th - March 10th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The core focus will be on shotgun proteomics data. Quantification through isobaric labels (iTRAQ, TMT) and label-free precursor peptide (MS1) ion intensities will also be introduced. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon your return from the course. An introduction to available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses. In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories. The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics. Note: this is a highly interactive course. It requires that the participants interact with each other and with the course instructors, in order to reach the learning outcomes in full. Course Pre-requisites The participants should have a basic knowledge about mass spectrometry based proteomics. Experience in analyzing proteomics data is an advantage, but not mandatory. The course does not require advanced computer skills. 2017-03-06 09:30:00 UTC 2017-03-06 09:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 2781-901 Mass spectrometry Proteomics Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt [] [] 20 workshops_and_courses registration_of_interest []
  • RNA-seq, 1 hp

    13 - 16 March 2017

    Elixir node event
    RNA-seq, 1 hp https://tess.elixir-europe.org/events/rna-seq-1-hp-bb9f6240-741a-4ea8-aa48-deda7e1198b4 Course content This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis. Topics covered will include: Gene and isoform detection using short RNA-seq reads Gene and isoform detection using long RNA-seq reads Gene and isoform detection combining RNA-seq data with other data sources Quality assessment of RNA-seq data Differential expression analysis using RNA-seq data on multiple cells Downstream analysis after identifying differentially expressed genes. 2017-03-13 09:00:00 UTC 2017-03-16 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • PGDH17 Population Genetics and Demographic History: model-based approaches

    13 March 2017

    Oeiras, Portugal

    Elixir node event
    PGDH17 Population Genetics and Demographic History: model-based approaches https://tess.elixir-europe.org/events/pgdh17-population-genetics-and-demographic-history    IMPORTANT DATES for this Course    Deadline for applications: Mar 6th 2017 (New)    Course date: March 13th - March 17th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description Genetic and genomic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic and genomic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this five-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to infer demographic history. We will learn how to perform coalescent simulations of genetic/genomic data (using SPAms and ms). We will also show how to simulated data for PSMC analyses. This will allow users to compare the PSMC obtained with real data to those obtained for the models they used. We will also look at how habitat fragmentation can be simulated using an in-house program. Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Course Pre-requisites Basic molecular population genetics and molecular ecology. Basic R knowldedge. Basic knowledge of genomic data. 2017-03-13 09:30:00 UTC 2017-03-13 09:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 2781-901 Genomics Population genetics [] bicourses@igc.gulbenkian.pt [] [] 20 workshops_and_courses registration_of_interest []
  • R Programming Foundations for Life Scientists, 2 hp

    27 March - 1 April 2017

    Elixir node event
    R Programming Foundations for Life Scientists, 2 hp https://tess.elixir-europe.org/events/r-programming-foundations-for-life-scientists-2-hp-56fa30d4-110b-45eb-a88c-682e65f58c51 Course content The course is addressed to life scientists with little or moderate experience in programming but enthusiastic about learning how to use R to make their work smoother and easier. The course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting with some more attention paid to the parts useful for life scientists. After introductory lectures on good programming practices, basic software design theory and a brief overview of R, we will delve into programming. We start by learning how to use R as a simple calculator, what are variable types, how to use data structures, how to implement repeating actions with and without loops, how to take actions based on certain condition. We gradually proceed to loading data, importing data from common file formats, we do some basic matrix algebra; learn how to perform basic statistical tests and how to visualize results. We will also put stress on giving you tools to access help and information on R-related challenges and issues, we will spend some time on learning how to install external packages, how to find bugs and address common installation issues. We also mention some more advanced topics and tell you more about BioConductor that is an invaluable tool for a computational biologist. You will also learn how to document your work and how to generate automatic reports. We try to illustrate all these concepts with some real-life examples and interesting lab tasks. The course will be given by experienced computational biologists from SciLifeLab and Uppsala University. Dr. Marcin Kierczak responsible for the content of the course is an experienced R user/coder, who has previously developed R packages and has experience in teaching programming and R to different audiences. 2017-03-27 09:00:00 UTC 2017-04-01 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • ABSTAT17 - Advanced Biostatistics for Bioinformatics Tool Users using R

    9 April 2017

    Portugal

    Elixir node event
    ABSTAT17 - Advanced Biostatistics for Bioinformatics Tool Users using R https://tess.elixir-europe.org/events/abstat17-advanced-biostatistics-for-bioinformatics-tool-users-using-r    IMPORTANT DATES for this Course    Deadline for applications: April 3rd 2017    Course date: April 10th - 13th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course description This course is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples. We will be using custom-built R scripts and packages that are available from the CRAN and/or Bioconductor repositories. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Methodology This intensive course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from biological data. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. Target Audience Everybody using Bioinformatics methods is implicitly using statistical methods. Moreover, proper judgement of the results often calls for a deeper level of understanding than what is required to solve scholarly exercises. We will look into particular areas such Simulation, Bayesian Inference, Hidden Markov Chains and Multivariate Data Analysis methods with the attitude, eyes and brains of an experienced statistician that wants to understand how the methods work and systematic way. Course Pre-requisites Intermediate level knowledge in Statistics is necessary. There is no time to provide basic knowledge, so we will need to assume that accepted candidates have self-assessed for it in the following areas: - probability - conditional probability - distributions - statistical tests - hypothesis testing - inference A suitable candidate will need to be able to answer 8 out of the 10 questions readily, without help. --> This level can also be obtained by attending another course in GTPB: The IBSTAT course. Basic Familiarity with the R environment will be necessary. Please follow the exercise that we provide. Install R from http://cran.r-project.org/ following the instructions. Download and unzip the Tutorial folder that is made available here. Then: - Visualize the slides in "Tutorial R.pdf" - Follow the exercise in "Basic_Exercise.pdf" - For reference, we also provide a script with a correct set of R statements in sequence "Tutorial_script.R" Additionally, we suggest that candidates acquire familiarity with RStudio by visiting the following resources: - Introduction to RStudio (basics) - Tutorial R and R Studio (complete) R Studio will be used in the course to ease-up interaction and increase productivity, but people that prefer the original R environment on the command line will be able to follow that preference. 2017-04-09 23:00:00 UTC 2017-04-09 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • ADER17 - Analysis of Differential Expression with RNAseq

    17 April 2017

    Oeiras, Portugal

    Elixir node event
    ADER17 - Analysis of Differential Expression with RNAseq https://tess.elixir-europe.org/events/ader17-analysis-of-differential-expression-with-rnaseq    IMPORTANT DATES for this Course   Deadline for applications: April 10th 2017   Course dates: April 17th - April 20th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course description Overview High-throughput technologies allow us to detect transcripts present in a cell or tissue. This course covers practical aspects of the analysis of differential gene expression by RNAseq. Participants will be presented with real world examples and work with them in the training room, covering all the steps of RNAseq analysis, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. We we will also cover some of the initial steps of secondary analysis, such as functional enrichment of the obtained gene lists. Target Audiences Life Scientists who want to be able to use NGS data to evaluate gene expression (RNAseq). Computational researchers that wish to get acquainted with the concepts and methodologies used in RNAseq are also welcome. Participants are encouraged to bring their own data and will have the opportunity to apply the concepts learned in the course. Pre-requisites Familiarity with elementary statistics and a few basics of scripting in R. Please have a look at the following resources and gauge your ability to use R in statitics at the basic level: Introduction to Data Science with R Videos from Coursera's four week course in R Statistics at Square One - BMJ Basic Unix command line skills, such as being able to navigate in a directory tree and copy files. See, for example, "Session 1" of the Software Carpentry training for a Unix introduction (Shell-novice material from the Software Carpentry Foundation). 2017-04-17 07:30:00 UTC 2017-04-17 07:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 1000-029 Transcriptomics RNA-Seq [] bicourses@igc.gulbenkian.pt [] [] 20 workshops_and_courses registration_of_interest []
  • ELB17F Entry Level Bioinformatics

    11 May 2017

    Portugal

    Elixir node event
    ELB17F Entry Level Bioinformatics https://tess.elixir-europe.org/events/elb17f-entry-level-bioinformatics    IMPORTANT DATES for this Course   Deadline for applications: May 1st 2017   Course date: May 8th - May 12th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview This is an entry level course aimed that those with a reasonable biological background butno significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Objectives The operation of the various programs used in the exercises will be explained, but only to the extent that allows a user to select parameters intelligently and to interpret results. The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations with a relatively high degree of user independence. In the training course design, this is intentionally built-in, to allow us to show a wide range of analytical techniques while providing enough experience to break the ice in all of them. Target Audience This course is intended for those wishing to investigate how they might begin to exploit the ever expanding abundance of computing and data resources for researchers seeking help in using them. Course Pre-requisites Basic understanding of molecular biology. No particular computing expertise will be assumed. 2017-05-11 23:00:00 UTC 2017-05-11 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • RODS17 Reproducible, Open Data Science

    20 June 2017

    Portugal

    Elixir node event
    RODS17 Reproducible, Open Data Science https://tess.elixir-europe.org/events/rods17-reproducible-open-data-science    IMPORTANT DATES for this Course    Deadline for applications: June 16th, 2017    Course date: June 21st - 23rd 2017 Course description In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this three day course, we will introduce to you the three organizing principles and practices that undergird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files.   Target Audience Researchers and Students in all sectors of Biomedicine. Pre-course Reading W S Noble. 2009. A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424 https://doi.org/10.1371/journal.pcbi.1000424 E M Hart et al. 2016. Ten Simple Rules for Digital Data Storage. PLoS Comput Biol 12(10): e1005097 https://doi.org/10.1371/journal.pcbi.1005097 P E Bourne et al. 2017. Ten simple rules to consider regarding preprint submission 13(5): e1005473. https://doi.org/10.1371/journal.pcbi.1005473   2017-06-20 23:00:00 UTC 2017-06-20 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2780-156 [] [] [] [] [] []
  • IBSTATB17 - Introductory Biostatistics for Biologists

    10 September 2017

    Portugal

    Elixir node event
    IBSTATB17 - Introductory Biostatistics for Biologists https://tess.elixir-europe.org/events/ibstatb17-introductory-biostatistics-for-biologists This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques in Biostatistics. Participants can expect to go through a set of exercises that are based on biomedical problems. These exercises are preceded by short lectures that are simple to follow. The lectures are designed to provide the conceptual framework that is needed to release the training power of the exercises, not to flood the participants with formality, which will be kept to a minimum. We will make use of a highly interactive methodology, taking advantage of our well equipped Bioinformatics training room. With this approach, we expect to bring the participants to a high degree of usage independence in using the methods that we cover. Main topics: Descriptive Statistics; Probability; Statistical Inference; Design of Experiments. Target Audience: Most participants must have had one or more semester courses in Statistics in their graduate education. For some, learning Statistics has happened a long time ago, and that makes it difficult to go back and manipulate the concepts with full confidence. For others, school days were just a while ago, but using that knowledge represents a serious effort. Opening a Statistics handbook, when you want to use Statistics righ away, is usually a painful experience, as concepts often show a less than obvious interdependence. Attending this course is a chance of revisiting those subjects in a systematic way, through a series of hands-on exercises, in a workflow that brings-in the skills in a seamless way. Course Pre-Requisites: Basic knowledge in Statistics is handy. Elementary skills in computer usage are needed. Basic Familiarity with the R environment will be necessary. Please follow the exercise that we provide. Install R from http://cran.r-project.org/ following the instructions. Download and unzip the Tutorial folder that is made available here. Then: Visualize the slides in "Tutorial R.pdf" Follow the exercise in "Basic_Exercise.pdf" For reference, we also provide a script with a correct set of R statements in sequence "Tutorial_script.R" Instructors:​             Ana Luísa Papoila holds a degree in Mathematics (Probability and Statistics) from the Faculdade de Ciências da Universidade de Lisboa (FCUL), a Master of Science in Statistics and Optimization, from the Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa (UNL) and a PhD in Statistics and Operational Research, in the field of Probability and Statistics, from the FCUL in 2006. Since then, she is an Assistant Professor in the NOVA Medical School / Faculdade de Ciências Médicas of UNL where she coordinates and teaches several undergraduate and postgraduate courses in Biostatistics. Her main areas of research interest are Applied Health Statistics and Epidemiology. She is an integrated member of the Centro de Estatística e Aplicações da Universidade de Lisboa (CEAUL) since 2007. She is also responsible for the area of statistics of the Division of Statistics and Epidemiology from the Research Center of Centro Hospitalar de Lisboa Central. In GTPB, she has been an instructor of the IBSTAT series, since 2014.            Affiliation: NOVA Medical School / Faculdade de Ciências Médicas of UNL, Lisboa, PT   Maria Fernanda Diamantino is an Assistant Professor at the Faculdade de Ciências da Universidade de Lisboa (FCUL) where she teaches since 1989. She obtained a Master of Science in Probability and Statistics (in the epidemiology area) and her PhD in Probability and Statistics in 2008, both at FCUL. Over the years, she has taught several undergraduate statistical courses in various areas, for example, biology, chemistry, geology, mathematics and informatics. She is a collaborator member of the Centro de Estatística e Aplicações da Universidade de Lisboa (CEAUL). She has been focusing her interests in biostatistics and applied health statistics and has taught postgraduate courses in those areas. In GTPB, she has been an instructor of the IBSTAT series, since 2014.             Affiliation: Faculdade de Ciências da Universidade de Lisboa, Lisboa, PT   Program: You can find here the detailed program.   Registration:  Register using here until August the 30th   Contact: For any questions about this course, please contact Pedro Fernandes (e-mail address below) 2017-09-10 23:00:00 UTC 2017-09-10 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • IO17 - Large-scale bioinformatics for Immuno-Oncology

    19 September 2017

    Portugal

    Elixir node event
    IO17 - Large-scale bioinformatics for Immuno-Oncology https://tess.elixir-europe.org/events/io17-large-scale-bioinformatics-for-immuno-oncology The immuno-oncology approach leverages on the unique capability of the immune system to recognize and kill tumour cells. This action is hampered by escape mechanisms put in place by tumour cells like, for instance, the engagement immune checkpoints, i.e. inhibitory molecules that modulate the amplitude and duration of immune responses. Immunotherapies that block checkpoint molecules are amongst the most promising approaches in immuno-oncology for the enhancement of antitumour immunity. Thanks to high-throughput technologies, such as next-generation sequencing (NGS) and proteomics, we have now access to large-scale tumour data that can be used to investigate the interplay between tumour and immune cells and the role of the immune system in tumour progression and response to therapy. In this course, you will learn to use bioinformatics tools and mathematical modelling techniques operating on high-throughput tumour data, in order to extract features that can be used to characterise this complex tumour-immune cell interface, such as: tumour antigens recognized by T cells tumour-infiltrating immune cells deregulated signalling pathways in cancer and immune cells A fully practical, hands-on approach will ensure that the newly acquire skills can be used with a great deal of autonomy. Target Audience: Motivated researchers, clinicians, and students who want to gain an understanding on how bioinformatics tools and simple (logic-based) modelling approaches can be used to investigate the tumour-immune cell interface and its underlying signalling pathways from high-throughput data. Course Pre-Requisites: Programming/scripting skills are helpful, but not mandatory. An understanding of elementary operations with R will be required. Elementary command line instructions in UNIX will be used, so minimal familiarity with navigation in directory trees, copying files and folders, etc. will be needed.  Instructors:​             Francesca Finotello received her PhD in Bioengineering in 2014 from the Department of Information Engineering, University of Padova (Italy). Her PhD thesis, entitled "Computational methods for the analysis of gene expression from RNA sequencing data", was awarded with the "Marco Ramoni" doctoral research award by the Italian National Bioengineering Group. She has an extensive experience on computational methods for the analysis of different types of next-generation sequencing (NGS) data, including RNA-seq and 16S ribosomal RNA gene sequencing of the human microbiota. Currently, she is a postdoctoral researcher in the Division of Bioinformatics of Medical University of Innsbruck (Austria). She is interested in bioinformatics and computational biology for cancer immunology and precision medicine, with a particular focus on in silico prediction of tumor neoantigens and deconvolution of tumour-infiltrating immune cells from NGS data. She is principal investigator of the research project "QuanTIseq: dissecting the immune contexture of human cancers" funded by the Österreichischen Krebshilfe Tirol (Austria) and aimed at developing a computational tool for the quantification of immune cell fractions from RNA-seq data of cell mixtures.            Affiliation: Division of Bioinformatics, Medical University of Innsbruck, AT   Federica Eduati received her PhD in Bioengineering in 2013 from the University of Padova, with a thesis (awarded the "Paolo Durst" best Italian PhD Thesis Award in Bioengineering) focusing on mechanistic modelling aspects of both large- and small-scale biological systems. In 2009 she participated to the DREAM4 "Predictive signaling network modeling" challenge classifying as best performing team. In 2011-2012 she was a visiting predoctoral fellow for 8 months in the Systems Biomedicine group at EBI. Since February 2013 she is a Postdoctoral EIPOD fellow - Marie Curie Fellow at EMBL (UK and Germany). Since May 2016 she is also a visiting scientist at JRC-COMBINE in RWTH Aachen (Germany). Currently, her main research interest is the investigation of why patients differentially respond to cancer therapy and how we can suggest personalized therapy. In particular, she is interested in approaching this problem by investigating signalling pathways, their deregulation in cancer and the specific effect of targeted therapy, using dynamic mathematical modelling approaches and machine learning techniques. She has also been working on the development of a microfluidics platform, which allows drug screening of live cells obtained from patient biopsies in a fast and cost-effective way. In 2013 she was also co-organizer of the NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge, where 213 registered participants from more than 30 countries had to predict cell line-specific cytotoxicity to chemical compounds based on genomic data and chemical attributes.            Affiliation: European Molecular Biology Laboratory (EMBL), Heidelberg, DE; JRC-COMBINE (RWTH Aachen), Aachen, DE   Program: You can find here the detailed program.   Registration:  Register using here until August the 30th   Contact: For any questions about this course, please contact Pedro Fernandes (e-mail address below) 2017-09-19 23:00:00 UTC 2017-09-19 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • EMBL-EBI Bioinformatics Workshop

    1 October 2017

    Portugal

    Elixir node event
    EMBL-EBI Bioinformatics Workshop https://tess.elixir-europe.org/events/embl-ebi-bioinformatics-workshop In this course, participants will receive an introduction to EMBL-EBI and its public data resources, with a focus on functional genomics (e.g. microarray expression profiling, RNA-seq, ChIP-seq).  During the course,participants will acquire skills in the effective use of functional genomics databases: ArrayExpress (one of the ELIXIR core data resources) and Expression Atlas.  Such skills will include searching, retrieving and interpreting data relevant to their research areas of interests.  There will be interactive presentations, demonstrations and practical exercises to give trainees hands on experiences.To complement the sessions on functional genomics, there will be brief presentations on some related EMBL-EBI resources: EBI metagenomics and Reactome.  Since many EMBL-EBI resources are built to facilitate reproducible research, there will also be a session discussing the obstacles and barriers to data reproducibility in the research environment, illustrated by real-life examples.  Participants will learn about some handy data management techniques that help to alleviate reproducibility problems, many of which have already been implemented for over a decade at EMBL-EBI. Please note this course does not cover microarray, sequencing, metagenomic or network data analysis.   Course Organizers:​ Cymon Cox is a senior researcher at  CCMAR in Faro. He is the leader of  the Plant Systematics and Bioinformatics group.             Affiliation: Fundação para a Ciência (FCT) / CCMAR, Faro, PT   Amy Tang studied Human Genetics at the University of Nottingham for her bachelor degree.  She did her PhD at the Brockdorff's lab, then at MRC Clinical Sciences Centre / Imperial College London, working on the epigenetic control of X-chromosome inactivation in mouse early development. The project was split 50:50 into wet-lab and bioinformatics, this is when she first got interested in bioinformatics. After a short postdoc in the same lab, she returned to study at Imperial for a MSc in Bioinformatics and Systems Biology, which helped her move laterally from wet-lab to bioinformatics. Amy now leads the curation efforts for ArrayExpress and Expression Atlas databases in the Gene Expression Team, promoting reproducible research by maintaining curation quality, and also by driving the development of the user-friendly ArrayExpress data submission tool Annotare. To allow users make the most out of the databases and to educate researchers on best practices for reproducible research, she also manages all training activities for the Team, delivering most of the hands-on courses on functional genomics resources at EMBL-EBI and worldwide.  Through listening to Annotare submitters' needs and gathering feedback at training courses, she also acts as users' advocate and works with software developers to improve user experience of ArrayExpress and Expression Atlas websites. Before joining EMBL-EBI, Amy was a senior bioinformatician in the Ensembl GeneBuild team, curating gene models for key model organisms such as mouse and rat.           Affiliation: EMBL-EBI, UK   Adelino V. M. Canário is a full professor at University of Algarve (Portugal) is a specialist in fish physiology. He is the Director of the Centre of Marine Sciences (ccmar.ualg.pt) since 1994 and leads the Comparative and Molecular Endocrinology research group. He teaches Cell Biology to undergraduate students and Reproductive Biology to graduate students. He coordinates courses for graduate students on Molecular and Cellular Biology Techniques and marine Genomics. He is the promoter of 2 ongoing PhDs and has supervised to completion 12 PhDs (8 in the last 5 years). He is internationaly recognized expert in his field with over 140 published articles (H=26) in regulation of calcium homeostasis, fish reproductive physiology, hormone-behavour relationships, chemical communication and genomics. He has coordinated and participated in European Commission funded research including recently Marine Genomics Europe, Assemble and EMBRC (ESFRI infrastructure).           Affiliation: Fundação para a Ciência (FCT) / CCMAR, Faro, PT   Grace Mugumbate Scientific Training Officer - Training           Affiliation: EMBL-EBI, UK   Course Lecturers:​ Steven Jupe is a Knowledge Database Curator/Developer for the Hermjakob team at the EML-EBI.            Affiliation: EMBL-EBI, UK   Amy Tang (Bio above)           Affiliation: EMBL-EBI, UK   Audience: This course is aimed at wet-lab researchers who have minimum or no prior experience in bioinformatics, who want to explore, and use EMBL-EBI resources for their research. No knowledge of programming is required, but the trainer expects an undergraduate level knowledge of biology and/or biochemistry.   Modules and resources: During this course, you will learn about: EMBL-EBI data services: an overview of the free databases and data services covering a wide range of subject areas across biological sciences. ArrayExpress: a public archive of functional genomics data (e.g. expression microarrays, RNA-seq, ChIP-seq), often deposited as a pre-requisite of journal publication Expression Atlas: a public resource of systematically analysed gene and protein expression data from manually curated studies across many species (not limited to model organisms) Data management: the problems we face in poor reproducibility of published research results, and how to alleviate them with some simple data management techniques   Learning Outcomes: After this course, you should be able to: Define some of the public data services EMBL-EBI provides Explore functional genomics data in ArrayExpress effectively, and submit your own data with ease. Search for and interpret expression information using Expression Atlas Discuss the value of biocuration in safeguarding reproducibility of research data   Program: Time Topic Lecturer Day 1 - 2nd October 2017 09:00 - 09:30 Welcome and Introduction to EBI resources Amy Tang 09:30 - 10:30 ArrayExpress Amy Tang 10:30 - 11:00 Tea/coffee break   11:00 - 12:30 ArrayExpress Amy Tang 12:30 - 13:30 Lunch   13:30 - 14:30 ArrayExpress and data submission Amy Tang 14:30 - 15:00 Tea/coffee break   15:00 - 16:00 An introduction to EBI Metagenomics Amy Tang 16:00 - 17:00 Data management for reproducible research Amy Tang 17:00 End of Day 1   Day 2 - 3rd October 2017 09:00 - 10:30 Expression Atlas Amy Tang 10:30 - 11:00 Tea/coffee break   11:00 - 12:30 Expression Atlas Amy Tang 12:30 - 13:30 Lunch   13:30 - 15:00 Expression Atlas & RNAseq-er API Amy Tang 15:00 - 15:30 Tea/coffee break   15:30 - 16:30 Reactome (webinar) Steve Jupe (TBC) 16:30 - 17:00 Wrap up and feedback Amy Tang 17:00 End of course       Participation: Participation has a 50€ registration fee. Registration for this course is done at the Centre for Marine Sciences (CCMAR) , until September the 28th! A maximum of 20 participants will be accepted. If you require assistance in finding accommodation, please contact Cymon J. Cox (e-mail bellow). 2017-10-01 23:00:00 UTC 2017-10-01 23:00:00 UTC Centre for Marine Sciences (CCMAR), Portugal Centre for Marine Sciences (CCMAR) Portugal 8005-139 [] [] [] [] [] []
  • Quality Assurance and Quality Control in Metabolomics

    12 - 13 October 2017

    Birmingham, United Kingdom

    Elixir node event
    Quality Assurance and Quality Control in Metabolomics https://tess.elixir-europe.org/events/quality-assurance-and-quality-control-in-metabolomics-ea29a17f-d41e-4488-808b-b137b7c82b93 This 2-day course will provide a comprehensive theoretical overview and hands-on experience of the application of quality assurance (QA) and quality control (QC) in metabolomics. It will include both theoretical and practical components to provide hands-on experience of using the mass spectrometer (a maximum of 4 people working on the instrument in a session) and the analysis of data. Experts who have developed the application of QA and QC procedures within the field will lead the course. 2017-10-12 09:00:00 UTC 2017-10-13 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Genome assembly and annotation course 3

    23 - 27 October 2017

    Oeiras, Portugal

    Elixir node event
    Genome assembly and annotation course 3 https://tess.elixir-europe.org/events/genome-assembly-and-annotation-course-3 ELIXIR Genome assembly and annotation course 3, Oct 23-27 2017 at the Gulbenkian Institute of Science, Oeiras, Portugal 2017-10-23 09:00:00 UTC 2017-10-27 17:00:00 UTC ELIXIR PT, Instituto Gulbenkian Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal Genomics Instituto Gulbenkian de Ciência [] life scientistsResearchersPhD students workshops_and_courses registration_of_interest genomics AssemblyTrainingeLearningEeLP
  • PM17 - Precision Medicine

    14 November 2017

    Portugal

    Elixir node event
    PM17 - Precision Medicine https://tess.elixir-europe.org/events/precision-medicine The implementation of cancer genomics into the clinic is becoming a reality. Personalized medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour.  Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Target Audience: This course is intended for working healthcare professionals and Bioinformaticians working in the area. Course Pre-Requisites: The course assumes that attendees are not intimidated by the prospect of gaining experience working on UNIX-like operating systems (including the shell, and shell scripting). Attendees should understand some of the science behind high-throughput DNA sequencing and sequence analysis, as we will not go deeply into underlying theory (or the mechanics of given algorithms, for example) as such. What will be taught are technical solutions for automating and sharing such analyses in reusable compute environments, which will include (but is not limited to) beginner-level programming, and basic Linux provisioning. General computer literacy, (e.g. editing plain text data files, navigating using the command line) will be assumed. (*)  (*) Note: An optional free session will be arranged with the participants that may be interested, on the EVE of the first day (Monday, Nov 13th at 4PM), where we will ensure that every participant willing to attend can use the Linux operating system at the required level. Instructors:​             Fátima Al-Shahrour obtained her PhD from Universidad Autónoma de Madrid (UAM) in 2006. During her PhD she worked at the Bioinformatics Unit at Spanish National Cancer Research Center (CNIO, Madrid, Spain) and Centro de Investigaciones Príncipe Valencia (Valencia, Spain). During this period, her research work dealt with the development of new Bioinformatics tools for microarray gene expression analysis, with a particular focus on computational methods for the functional interpretation of high-throughput experiments. In 2007, she joined the Computational Biology and Bioinformatics group at Cancer Program at Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard (Cambridge, USA). In 2008, she got a staff position at Broad Institute of MIT and Harvard as a Computational Biologist. During this period, her research was focused on the study the biology and treatment of cancer under a genomic perspective using hematopoiesis as a model system. In 2012 she joined the Spanish National Cancer Research Centre (CNIO) to lead the Translational Bioinformatics Unit (TBU) in the Clinical Research Programme and since 2017 she is leading the Bioinformatics Unit (BU). -- The CNIO Bioinformatics Unit (BU) belongs to the Structural and Biocomputing Programme. This is a group with a large trajectory in bioinformatics for functional genomics, field in which the group has published numerous papers as well as developed distinct applications and programs widely used by the scientific community. BU's major research activity is focused on the development of new computational methodologies to perform genomic analysis of cancer patients' data, in order to identify new biomarkers and mechanisms of drug response. The main goal is to translate this knowledge into effective treatments for cancer patients. Since 2013, we extensively collaborate with hospitals to analyze next-generation sequencing data from patient's tumors. During this period, we have applied our analytical pipeline for the categorization and interpretation of patient's tumors and match them to effective drugs or treatments based on their genomic alterations.            Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES Javier Perales is a PhD student working under the supervision of Fátima Al-Shahrour & Alfonso Valencia, at the Spanish National Cancer Research Centre. During his education, he has acquired knowledge in Molecular Biology, Genetics and Computational Biology. His research activity is focused on the genomic characterization of patient tumours by Next-Generation Sequencing technologies. He is interested on the development and integration of computational approaches for cancer genomics data in order to improve our understanding about the individual patient's disease.            Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES Elena Piñeiro is a Bioinformatician working in the Bioinformatics Unit of the CNIO. Her work is mainly focused on the elaboration of pipelines for the analysis and prioritization of genomic variations obtained through NGS technologies and on the construction of a methodology for the personalized drug assignation according to the particular genomic profile of each patient.            Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES   Program: You can find here the detailed program.   Registration:  Register using here until October the 18th   Contact: For any questions about this course, please contact Pedro Fernandes (e-mail address below) 2017-11-14 09:00:00 UTC 2017-11-14 00:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • GOBLET AGM 2017

    22 November 2017

    Portugal

    Elixir node event
    GOBLET AGM 2017 https://tess.elixir-europe.org/events/goblet-agm-2017 The Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) is holding its 6th annual general meeting in Oeiras, Portugal.    Program: The latest version of the agenda can found here. The provisional agenda is as follows: Time Wednesday, 22nd Thursday, 23rd Friday, 24th 09:00-09:15 Welcome & Logistics Defining Standards for Training Materials Currency and Advancement in Trainer Skills 09:15-10:30 GOBLET AGM Matters 10:30-11:00 Coffee Break Coffee Break Coffee Break 11:00-12:30 GOBLET Committee Reports Defining Standards for Training Materials (cont.) Currency and Advancement in Trainer Skills (cont.) Action Plan for the upcoming year Closing and Wrap-up 12:30-13:30 Lunch Lunch Lunch 13:30-15:00 GOBLET AGM 2018 AOB Draft Publication on Bioschemas activity   15:00-15:30 Coffee Break 15:30-16:00 Draft Publication on Bioschemas activity (hands-on) 16:00-17:30 Adjourn 17:30- Adjourn   Registration: Participation requires registration.   Register using this form  Book your stay at Hotel Solar Pameiras by e-mail, stating that you are attending GOBLET2017 to get our discounted rate (Eur 60.00 per night) Mailto: Reservas Solar Palmeiras More information here. 2017-11-22 09:00:00 UTC 2017-11-22 00:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2780-156 [] [] [] [] [] []
  • ELB18F Entry Level Bioinformatics (First course in 2018)

    19 February 2018

    Portugal

    Elixir node event
    ELB18F Entry Level Bioinformatics (First course in 2018) https://tess.elixir-europe.org/events/elb18f-entry-level-bioinformatics-first-course-in-2018 Overview This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Objectives The operation of the various programs used in the exercises will be explained, but only to the extent that allows a user to select parameters intelligently and to interpret results. The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations with a relatively high degree of user independence. In the training course design, this is intentionally built-in, to allow us to show a wide range of analytical techniques while providing enough experience to break the ice in all of them. 2018-02-19 09:00:00 UTC 2018-02-19 00:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • NERC-MDIBL Environmental Genomics and Metabolomics 2018

    4 - 9 March 2018

    Birmingham, United Kingdom

    Elixir node event
    NERC-MDIBL Environmental Genomics and Metabolomics 2018 https://tess.elixir-europe.org/events/nerc-mdibl-environmental-genomics-and-metabolomics-2018 This NERC funded short course will provide a hands-on approach to guide genomics and metabolomics research applied to the environmental scientists. Participation in the course is open to everyone but priority is given to NERC-funded PhD students and early-career scientists. The course will include ~1.5 days generic environmental omics training and ~3.5 days specialized genomics or metabolomics training. Case studies using multi-omics data will be provided so that you gain practical experience of analyzing and interpreting multi-omics data. Distinguished visiting academics will provide keynote lectures on each day of the course to highlight environmental omics applictions that draw on the expertise of the guest faculty. 2018-03-04 09:00:00 UTC 2018-03-09 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT Genomics Metabolomics [] [] [] [] [] []
  • Tools for Reproducible Research

    22 - 24 March 2018

    Elixir node event
    Tools for Reproducible Research https://tess.elixir-europe.org/events/tools-for-reproducible-research #url https://www.scilifelab.se/events/reproducible-research-vt18/ #training Course leaders: Leif Wigge (leif.wigge@scilifelab.se) and Rasmus Ågren (rasmus.agren@scilifelab.se) Location: Air/Fire, Stockholm SciLifeLab National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities with interest in making their computational analysis more reproducible.  Responsible teachers: Leif Wigge, Rasmus Ågren Contact information: leif.wigge@scilifelab.se and rasmus.agren@scilifelab.se Apply here: https://www.scilifelab.se/events/reproducible-research-vt18/   2018-03-22 09:00:00 UTC 2018-03-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • RNA-seq

    14 - 17 May 2018

    Elixir node event
    RNA-seq https://tess.elixir-europe.org/events/rna-seq Course information: https://www.scilifelab.se/events/rnaseqvt18/ Course leader Johan Reimegård (johan.reimegard@scilifelab.se) #training Course content This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis. Topics covered will include: Gene and isoform detection using short RNA-seq reads Gene and isoform detection using long RNA-seq reads Gene and isoform detection combining RNA-seq data with other data sources Quality assessment of RNA-seq data Differential expression analysis using RNA-seq data on multiple cells Downstream analysis after identifying differentially expressed genes. Entry requirements Basic knowledge in linux is a requirement! We will not teach Linux at the course and you will have considerable trouble to follow the practical sessions if you are not reasonably used to work in a linux environment. Be able to bring your own laptop for the practical computational exercises. If you don’t have a laptop to bring please contact education@scilifelab.uu.se before you register. Some programming/scripting experience is desirable, but not required. Experience working on the SNIC center Uppmax is desirable, but not required. Participants of the SciLifeLab Course “Introduction to Bioinformatics using NGS data” (or alike) are most welcome to apply, but this course is not required. Some overlap with this course is expected, but the workshops will be considerably more detailed on the covered topics. Due to space constraints for the computer exercises, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Date and time 2017-11-07 - 2017-11-09 Location Husargatan 3, Uppsala Important dates Application open: June 19 Application deadline: September 28 Confirmation to accepted students: October 9 Responsible teachers: Johan Reimegård If you don’t receive information according to the dates above, contact education@scilifelab.uu.se Course fee A course fee of 1300 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.     2018-05-14 09:00:00 UTC 2018-05-17 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Genome Annotation

    15 - 18 May 2018

    Elixir node event
    Introduction to Genome Annotation https://tess.elixir-europe.org/events/introduction-to-genome-annotation Course Information: https://www.scilifelab.se/events/geneeann-vt18/ Course leader Henrik Lantz (henrik.lantz@nbis.se) #training Apply here: https://docs.google.com/forms/d/e/1FAIpQLSeOLov4kGj8t50KZSS7Tsc2TSuuj91ZY-E33Mw263pfBaXMsQ/viewform  Course content Genome annotation is the process in which loci of interest in a genome are identified, both in structure and function. The structural part includes identifying the number and size of exons and introns, size of UTRs, and number of isoforms. The functional annotation, in turn, focuses on inferring the biological role of different transcripts. The course is aimed at researchers that are involved in on-going or upcoming genome projects and wish to deepen their understanding of the various forms of data and computational steps required to achieve a comprehensive annotation. The focus of the course will be on non-model eukaryote organisms, and in particular the structural annotation of protein coding genes. We will use de novo gene finders, protein alignments and RNA-seq data to infer the structure of genes, and show how to combine these different lines of evidence to get the most stable and informative annotation. We will also infer the function of these genes using similarity to known proteins as well as the presence of functional domains. Topics covered will include: ·       Project planning ·       Gene finders ·       Protein alignment ·       RNA-seq assembly ·       Combined structural annotation using Maker2 ·       Functional annotation ·       Procaryote annotation ·       The NBIS annotation service Entry requirements Participants must be comfortable navigating a linux shell and execute programs from the command line. Without this knowledge, it will be impossible to participate in the computer exercises. Previous experience from working with NGS data (genome assembly, transcriptome assembly, SNP calling) is a plus. Applicants are also encouraged to bring their own laptops, but there will be computers to use for participants unable to do so. Due to space constraints for the computer exercises, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course. 2018-05-15 09:00:00 UTC 2018-05-18 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Single cell RNA sequencing data analysis

    21 - 24 May 2018

    Elixir node event
    Single cell RNA sequencing data analysis https://tess.elixir-europe.org/events/single-cell-rna-sequencing-data-analysis-2986aebb-b31b-499d-9bd0-e7cc04658a51 #url https://www.scilifelab.se/events/scRNAseq-VT18/ National course open for PhD students, postdocs, researchers and other employees in need of single cell RNA-seq data analysis skills within all Swedish universities Course name: Single cell RNA sequencing data analysis Course dates: 2018-05-21 to 2018-05-23 Course location: SciLifeLab, Tomtebodavägen 23A, 171 65 Solna Important dates Application opens: February 1 Application closes: April 23 Confirmation to accepted students: April 27 Responsible teachers: Åsa Björklund If you do not receive information according to the above dates please contact: asa.bjorklund@scilifelab.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and course dinner.. *Please note that NBIS cannot invoice individuals Course content This course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include: An overview of the current scRNAseq techniques Basic overview of pipelines for processing raw reads into expression values Quality control of scRNAseq data Dimensionality reduction and clustering techniques Data normalization Differential gene expression for scRNAseq data Examples on how to use these tools in a research project. Entry requirements Required for being able to follow the course and complete the computer exercises Basic knowledge in Linux is a requirement. We will not teach Linux at the course and you may have considerable trouble to follow the practical sessions if you are not reasonably used to work in a Linux environment. Be able to bring your own laptop with R installed for the practical computational exercises. Instructions on installation will be sent by email to accepted participants. Some programming/scripting experience is required (preferably in R). Desirable: Experience working on the SNIC center Uppmax is desirable, but not required. We encourage accepted participants to do an Uppmax tutorial before the course. Previous experience with RNA-seq analysis and/or participation in NGS/RNA-seq course is an advantage. Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Link to application: https://goo.gl/forms/89JPQcm0j7zKtjLN2 2018-05-21 09:00:00 UTC 2018-05-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    21 - 26 May 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-8ba319ee-3569-4b1f-839d-1f2cbc483a10 Course Information: https://www.scilifelab.se/events/ngsdatavt18lkp/ #training Course leader: Manfred Grabherr, manfred.grabherr@scilifelab.se and Malin Larsson, malin.larsson@scilifelab.se Course content The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs. Topics covered will include: Basic Linux usage NGS read-to-reference alignment (genomic and RNA-Seq) Variant calling in populations De novo assembly of RNA-sequence data Reference-guided RNA-Seq expression analysis Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data. Entry requirements A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable To get the maximum benefit from the course we would like you to Have relevant previous experience in sequencing or analysis Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing Be able to bring your own laptop for the practical computational exercises It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Important dates Application open: August 1 Application deadline: October 7 Confirmation to accepted students: October 23 Responsible teachers: Manfred Grabherr If you don’t receive information according to the dates above, contact education@scilifelab.uu.se Course fee A course fee of 1800 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.   2018-05-21 09:00:00 UTC 2018-05-26 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • PDA18 Proteomics Data Analysis

    27 May 2018

    Portugal

    Elixir node event
    PDA18 Proteomics Data Analysis https://tess.elixir-europe.org/events/pda18-proteomics-data-analysis Course description Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering peptide and protein identification, quantification, and differential analysis. Moreover, more advanced experimental designs and blocking will also be introduced. The core focus will be on shotgun proteomics data, and quantification using label-free precursor peptide (MS1) ion intensities. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon returning from the course. You will also learn how to submit data to PRIDE/ProteomeXchange, which is a common requirement for publication in the field, and how to browse and reprocess publicly available data from online repositories. The course will thus provide a solid basis for beginners, but will also bring new perspectives to those already familiar with standard data interpretation procedures in proteomics. Note: This is a highly interactive course. It requires that the participants interact with each other and with the course instructors, in order to reach the learning outcomes in full. Program: You can see the detailed program through the link below. Detailed Program  Registration:  Register until May 23rd, following the instructions in the link below.  Application Instructions  Contact: For any questions regarding this course, please contact GTPB (contacs below) 2018-05-27 23:00:00 UTC 2018-05-27 23:00:00 UTC Instituto Gulbenkian de Ciencia, Portugal Instituto Gulbenkian de Ciencia Portugal 2780-156 [] [] [] [] [] []
  • RaukR, Advanced R for Bioinformatics, Summer course

    10 - 22 June 2018

    Elixir node event
    RaukR, Advanced R for Bioinformatics, Summer course https://tess.elixir-europe.org/events/advanced-r-for-bioinformatics-summer-school #training #url: https://www.scilifelab.se/events/raukr-advanced-r-for-bioinformatics-summer-school/ #url: https://nbisweden.github.io/workshop-RaukR-1806/  International course. The course is open for researchers at university or in industry such as PhD students, postdocs, group leaders, core facility staff and analysts. Course leaders: Marcin Kierczak (marcin.kierczak@scilifelab.se), Sebastian Dilorenzo (sebastian.dilorenzo@nbis.se) Course description Join us in medieval Visby this June to improve your R skills and have a nice time! In Life Science and Bioinformatics, R is increasingly being used to transform and analyse data, perform statistical analysis and produce publication-ready visualizations. This Summer course will focus on advanced R functionality, to increase the participants skillset and understanding of what is possible to do today. You are very welcome to apply or see the homepage for more information. Please, help us spread the word to interested participants! Guest speakers Martin Morgan (Director at Bioconductor) Paula Moraga (Lancaster Univ., RLadies) Yhui Xie (RStudio) Course content Reproducibility with R Writing R packages R scripts S3, S4 and Reference Classes Code debugging and optimization R markdown tidyverse Bioconductor ggplot2 Interactive plots Statistics in R Machine Learning Shiny web applications Working with maps Area specific workshops (RNAseq, spatial stats etc) Working with your own dataset Course fee Academic: 8500 SEK (Includes participation in all official activities and events, course materials, breakfast, lunch and accommodations). Participants from outside of academia should contact us for a fee quote. The fee does not include travel costs. Important dates  Application open: March 17 Application deadline: April 15 Notification of acceptance/decline: April 25 2018-06-10 09:00:00 UTC 2018-06-22 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Advanced Python programming

    11 - 16 June 2018

    Elixir node event
    Advanced Python programming https://tess.elixir-europe.org/events/advanced-python-programming #training More information will follow Course leader: Sergiu Netotea (sergiu.netotea@scilifelab.se) 2018-06-11 09:00:00 UTC 2018-06-16 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • DMOS18 Data Management and Open Science

    11 June 2018

    Portugal

    Elixir node event
    DMOS18 Data Management and Open Science https://tess.elixir-europe.org/events/dmos18-data-management-and-open-science Course Description   In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this four day long course, we will introduce to you the three organizing principles and practices that undergird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files. We will then steer the participants into good practices in data management and work on practical examples taken from published papers and data, showing how these practices influence replicability and reproducibility. At the end we will discuss publication bias and its consequences in current research quality. Program: You can see the detailed program through the link below. Detailed Program  Registration:  Register until June 7th, following the instructions in the link below.  Application Instructions  Contact: For any questions regarding this course, please contact GTPB (contacs below) 2018-06-11 23:00:00 UTC 2018-06-11 23:00:00 UTC Instituto Gulbenkian de Ciencia, Portugal Instituto Gulbenkian de Ciencia Portugal 2780-156 [] [] [] [] [] []
  • Metabolomics: Understanding Metabolism in the 21st Century

    23 July - 17 August 2018

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics: Understanding Metabolism in the 21st Century https://tess.elixir-europe.org/events/metabolomics-understanding-metabolism-in-the-21st-century Metabolomics is an emerging field that aims to measure the complement of metabolites (the metabolome) in living organisms. The metabolome represents the downstream effect of an organism’s genome and its interaction with the environment. Metabolomics has a wide application area across the medical and biological sciences. The course provides an introduction to metabolomics, describes the tools and techniques we use to study the metabolome and explains why we want to study it. By the end of the course you will understand how metabolomics can revolutionise our understanding of metabolism. 2018-07-23 09:00:00 UTC 2018-08-17 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    10 - 15 September 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-5ae594b9-4fa3-4e1e-addd-ec9cc2b6a98b #training More information will follow Course leader: Manfred Grabherr, manfred.grabherr@scilifelab.se  Course content The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs. Topics covered will include: Basic Linux usage NGS read-to-reference alignment (genomic and RNA-Seq) Variant calling in populations De novo assembly of RNA-sequence data Reference-guided RNA-Seq expression analysis Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data. Entry requirements A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable To get the maximum benefit from the course we would like you to Have relevant previous experience in sequencing or analysis Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing Be able to bring your own laptop for the practical computational exercises It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. 2018-09-10 09:00:00 UTC 2018-09-15 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Elixir-EXCELERATE Train-the-Trainer course

    9 - 12 October 2018

    Elixir node event
    Elixir-EXCELERATE Train-the-Trainer course https://tess.elixir-europe.org/events/elixir-excelerate-train-the-trainer-course #training ELIXIR-EXCELERATE, in collaboration with ELIXIR Sweden and ELIXIR-IIB, is pleased to announce a Train the Trainer (TtT) event. Course information/Course webpage: https://elixir-iib-training.github.io/website/2018/10/09/train-the-trainer-stockholm.html  Application form: https://docs.google.com/forms/d/e/1FAIpQLSc0KwSjcBJ6wemxCBhgDrfg4OxccFbbDM_ZA-0Ui4jEe_eV1Q/viewform  Important dates Course date: 9-11 October, 2018 We will accept a maximum of 20 participants. Priority will be given to candidates from ELIXIR Sweden and other ELIXIR nodes. Notifications of acceptance will be sent shortly after the application, which will remain open until we reach 20 participants. Venue Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden Room: Air Fee There is no course attendance fee. The participants will need to bear their travel, hotel (if any) and meal costs. Candidates from ELIXIR nodes might apply for an ELIXIR-EXCELERATE TtT Exchange Programme Travel Grant when they fill their application form. Instructors Allegra Via (Training Coordinator ELIXIR-IIB, IBPM-CNR) Jessica Lindvall (Training Coordinator ELIXIR-SE, NBIS) Local organisers Jessica Lindvall, NBIS (National Bioinformatics Infrastructure Sweden), Elixir-SE Description The course is made up of four sessions, covering: Learning principles and how they apply to training and teaching Teaching techniques that can be used to enhance learner engagement and participation Assessment and feedback in training and teaching Lesson, course, and materials design Application form Target Audience Whoever is interested in becoming a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you. How learning works? How can I use learning principles and theories to improve my teaching? How can I make my teaching more engaging and effective? How should I adjust my teaching to different types of learners? How can I help slow learners? How can I assess whether my students are actually understanding my lessons? Are they actually learning? What is the best balance between theory and practice? How can I best assess whether learning is occurring and/or has occurred? What works in a classroom and what doesn’t? How can I become a better teacher? Etc. Learning Objectives: To get acquainted with Learning principles and how they apply to training To be able to select and utilise training techniques that can be used to enhance learner engagement and participation To learn how to use assessment and feedback in training To learn about session, course, and materials design Learning Outcomes: Learners can name learning principles that a good teacher/instructor should have in mind Learners can describe at least three training techniques, drawing on learning principles Learners can design a training session and a course Learners can develop assessment questionnaires Learners can enumerate types of materials needed for each part of a training session or course Preliminary Programme TimeActivity DAY 1 10.00 - 10.30Introductions, who is who and what we need to achieve 10.30 - 12.30Session 1: Review of learning principles and how they apply to training and teaching 12.30 - 13.30Lunch time 13.30 - 14.30Cont. Session 1 14.30 - 17.00Session 2: Training techniques that can be used to enhance learner engagement and participation DAY 2 09.00 - 11.30Cont. Session 2 11.30 - 12.30Lunch time 12.30 - 15.30Session 3: Session, course, and materials design 15.30 - 17.00Session 4: Assessment and feedback in training DAY 3 09.00 - 11.30Cont. Session 4 11.30 - 12.00Wrap-up 2018-10-09 09:00:00 UTC 2018-10-12 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Data Carpentry Workshop

    14 October 2018

    Portugal

    Elixir node event
    Data Carpentry Workshop https://tess.elixir-europe.org/events/data-carpentry-workshop-281918cd-729d-4e32-b083-534121b23d5e The ELIXIR-PT/BioData.pt infrastructure and the Instituto Gulbenkian de Ciência (IGC) are proud to announce that a Data Carpentry Workshop, with a special focus on Genomics data, will be held at the IGC on October 15th and 16th 2018. For those unfamiliar with the concept, Data Carpentry aims at systematically delivering workshops on the fundamental data skills needed to conduct research. What you will learn will largely influence the way in which you handle data in a fully independent way, free from proprietary software and storage platforms. The workshop will be run by Mateusz Kusak and Paula Andrea Martinez, both highly qualified instructors of the Carpentries (https://carpentries.org/). The content will be the Genomics Curriculum https://datacarpentry.org/lessons/#genomics-workshop. Attendance will be granted for FREE to up to 30 participants that need to apply before October 5th at 12h00 using the Eventbrite page that will be provided via a link on the ELIXIR-PT/BioData.pt website (http://Biodata.pt/Events/DC2018) The conditions for attendance are specified in the following online document: https://datacarpentry.org/workshops-attend/ Eventbrite application form: http://www.eventbrite.com/e/elixir-ptbiodatapt-data-carpentry-workshop-tickets-50703819489   2018-10-14 23:00:00 UTC 2018-10-14 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2780-156 [] [] [] [] [] []
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