Register event
18 events found

Node: Germany 

  • CSAMA 2019 - Statistical Data Analysis for Genome-Scale Biology

    21 - 26 July 2019

    Brixen, Italy

    CSAMA 2019 - Statistical Data Analysis for Genome-Scale Biology https://tess.elixir-europe.org/events/csama-2019-statistical-data-analysis-for-genome-scale-biology Educators: Wolfgang Huber, Mike Smith, Vincent J. Carey, Laurent Gatto, Robert Gentleman, Martin Morgan, Johannes Rainer, Lori Shepherd, Charlotte Soneson, Levi Waldron Simone Bell (HD-HuB) Date: 21 to 26 July 2019 Location: Brixen, Italy Contents: The one-week intensive course Statistical Data Analysis for Genome-Scale Biology teaches statistical and computational analysis of multi-omics studies in biology and biomedicine. It covers the underlying theory and state of the art (the morning lectures) and practical hands-on exercises based on the R / Bioconductor environment (the afternoon labs). Learning goals: At the end of the course, you should be able to run analysis workflows on your own (multi-)omic data, adapt and combine different tools, and make informed and scientifically sound choices about analysis strategies. Prerequisites: The course is intended researchers who have basic familiarity with the experimental technologies and their applications in biology, and who are interested in making the step from a user of bioinformatics software towards adapting or developing their own analysis workflows. Keywords: Statistics, biology, RNASeq, Bioconductor, R, RStudio human genetics. Tools: R / Bioconductor 2019-07-21 09:00:00 UTC 2019-07-26 17:00:00 UTC de.NBI Brixen, Brixen, Italy Brixen Brixen Südtirol Italy [] [] [] workshops_and_courses [] []
  • Analyzing metabolic networks with CellNetAnalyzer - MPA

    12 August 2019

    Riga, Latvia

    Analyzing metabolic networks with CellNetAnalyzer - MPA https://tess.elixir-europe.org/events/analyzing-metabolic-networks-with-cellnetanalyzer-mpa Educators: Axel von Kamp, Philipp Schneider, Steffen Klamt (de.NBI-SysBio) Date: Monday, 12th of August 14:00 - 17:30 Location: Riga, Lativa, MPA Conference Contents: CellNetAnalyzer (CNA) is a MATLAB package for analyzing biological (metabolic, signaling and regulatory) networks and supports both command-line based operations as well as a graphical user interface with embedded network visualizations. In the first part of the tutorial (1,5h) we will demonstrate key features of CNA for stoichiometric and constraint-based modeling of metabolic networks (including flux (balance) analysis, flux and yield optimization, elementary mode analysis, computational strain design with minimal cut sets and others). The second part of the tutorial (1,5h) will consist of hands-on exercises where the participants will learn how to use CellNetAnalyzer in practice.. Prerequisites: Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration). Download and preinstallation of CellNetAnalyzer is recommended but not mandatory. Keywords: CellNetAnalyzer (CNA), SBML, modeling, kinetic data access, Tools: CellNetAnalyzer 2019-08-12 14:00:00 UTC 2019-08-12 17:00:00 UTC de.NBI Riga, Riga, Latvia Riga Riga Latvia [] [] [] meetings_and_conferences [] []
  • 2nd de.NBI Cloud User Meeting

    3 - 5 September 2019

    Heidelberg, Germany

    2nd de.NBI Cloud User Meeting https://tess.elixir-europe.org/events/2nd-de-nbi-cloud-user-meeting Educators: de.NBI Cloud Group Date: 03.09 to 05.09 Location: Heidelberg What is it about? The 2nd de.NBI Cloud User Meeting is an upcoming 3-day event (03.09.2018-05.09.2018) in Heidelberg for people interested in Bioinformatics, Cloud Computing or Big Data. Due to the diversity of approaches that arise in this exciting and rapidly evolving cloud computing technology niche, this meeting should help to exchange ideas and approaches in the growing de.NBI Cloud community. We aim to advantage our attendees, from beginner to expert, with comprehensive understanding of the very broad application and benefit of the de.NBI Cloud. This event is your chance of meeting users, developers and administrators using the de.NBI Cloud. We feature topics from introduction or use case talks to introduce different technologies (OpenStack, Docker, Kubernetes, Nextflow, ….) to tutorials and workshops that will help understand how to actually apply the technology in your research. Confirmed Speakers Matthias König – Humboldt-University Berlin Alan Beccati – Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy Alexander Peltzer – Quantitative Biology Center (QBIC) Johannes Werner – Leibniz-Institute for Baltic Sea Research Jens Preussner – Max Planck Institute for Heart and Lung Research Marius Dieckmann – Bioinformatics and Systems Biology, Justus University Giessen Björn Grüning – Bioinformatics Group Freiburg University Helena Rasche – Bioinformatics Group Freiburg University Jan Krüger – Computational Metagenomics, Bielefeld University Who should attend this meeting? We welcome people from all background, no matter if you are new to the de.NBI Cloud or considering to submit a project application, to learn and network in our growing community. What to bring? Laptop Preliminary Agenda: 03.09. (13:00 – 18:00): Presentation of use cases 04.09. (09:00 – 17:00): Workshop 05.09. (09:00 – 13:00): Workshop Registration Deadline 23.08.2019 Further Information and registration at https://cloud.denbi.de/2nd-de-nbi-cloud-user-meeting/ 2019-09-03 13:00:00 UTC 2019-09-05 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Dresden Deep Learning Hackathon

    9 - 13 September 2019

    Dresden, Germany

    Dresden Deep Learning Hackathon https://tess.elixir-europe.org/events/dresden-deep-learning-hackathon Educators: Florian Jug, Peter Steinbach, others (DAIS/CIBI) Date: 09.09.2019 – 13.09.2019 Location: SLUB, Klemperer-Saal Zellescher Weg 18 01069 Dresden Germany Contents: The Dresden Deep Learning Hackathon ( #d3hack2019 ) is meant to bring together machine learning experts and scientific practitioners. Teams of 2-4 scientists can apply for the hackathon given a scientific problem they want to solve with machine learning. Upon approval, they will be assisted by one or two machine learning experts for 5 days consecutively! This effort is meant to give your team a head-start and potentially create an end-to-end machine learning solution for your science. The teams are motivated to publish a scientific paper about the hackathon efforts at dedicated conferences or in established journals - at best jointly with their mentors - after the hackathon. A win-win situation for all parties involved. The scope of scientific domains that can apply is not limited. For sure, our mentors have a given background mostly with regard to 2D or 3D images. So we will try to match that as close as possible. However, we are still in the process of fixing mentors (we have expressions of interest of about 5 more than listed below). We will also consider a limited amount of applications using standard machine learning (MLP, SVM, RandomForests,...). If you are unclear whether your topic fits the hackathon, please reach out to us. Most importantly, any team without a readily available data set for training will be discarded from the candidate list. In other words, if you are interested in applying machine learning to your data, you shouldn't use the hackathon to annotate your data. The workshop admission fee amounts to € 300 per participant to cover room rent and catering. We are still looking for sponsors, so there is a non-negligible probability that the admission fee will be reduced in the future. The call for applications closes on June 30, 2019, at 12pm AoE! After this date, a review board of mentors and organizers will judge the applications and send out confirmations to the applications until mid July the latest. The registration mechanism of participants will be circulated then. For members of non-academic institutions: We cannot allow applications from non-academic institutions or industry to our hackathon. If you want to participate with a project as a company, this project needs to be embedded in a scientific group and the majority of team members need to be employed by a scientific institution. On top, the results of the hackathon are expected to be published. So be prepared to undisclose your results and (at best) the data and code which produced these results. Learning goals: - Fundamentals of deep learning with CNNs. - Keras API with the Tensorflow backend. - How to define your deep net. - How to train it. Prerequisites: Bring your own laptop. Keras and Tensorflow backend should already be installed. (We will have GPU nodes you can use if your laptop does not offer a fast GPU.) Solid understanding of the fundamentals of linear algebra. Programming skills (never programmed… that will not work out, sorry!) Keywords: DeepLearning, Keras, Tensorflow, Python Tools: Keras, Python, Tensorflow 2019-09-09 09:00:00 UTC 2019-09-13 17:00:00 UTC de.NBI Dresden, Dresden, Germany Dresden Dresden Dresden Germany [] [] [] workshops_and_courses [] []
  • Combining Workflows, Tools and Data Management - GCB 2019

    16 September 2019

    Heidelberg, Germany

    Combining Workflows, Tools and Data Management - GCB 2019 https://tess.elixir-europe.org/events/combining-workflows-tools-and-data-management-gcb-2019 TBA 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • SeqAn3 – a modern C++ library for efficient sequence analysis - GCB 2019

    16 September 2019

    Heidelberg, Germany

    SeqAn3 – a modern C++ library for efficient sequence analysis - GCB 2019 https://tess.elixir-europe.org/events/seqan3-a-modern-c-library-for-efficient-sequence-analysis-gcb-2019 TBA 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Getting started with the de.NBI Cloud - GCB 2019

    16 September 2019

    Heidelberg, Germany

    Getting started with the de.NBI Cloud - GCB 2019 https://tess.elixir-europe.org/events/getting-started-with-the-de-nbi-cloud-gcb-2019 Educators: Alexander Sczyrba, Peter Belmann, Sebastian Jünemann, Jan Krüger, Alex Walender (BiGi) Location: Heidelberg GCB Date: 16th September Content: The need for high-throughput data analysis has grown tremendously since the introduction of next-generation sequencing (NGS) platforms. The massive amount of data produced creates a new class of resource barriers to be overcome including limited bandwidth, storage volume and compute power. Small research labs can hardly cope with the data generated. A solution to the mere resource problem are cloud computing environments as virtually unlimited and flexible resources. The de.NBI Cloud is a full academic cloud federation, providing compute and storage re-sources free of charge for academic users. It provides a powerful IT infrastructure in combination with flexible bioinformatics workflows and analysis tools to the life science community in Germany. The de.NBI Cloud offers reliable IT security concepts and user access rules to en-sure secure data access and storage. It closes the gap of missing computational resources for life science researchers in Germany. The de.NBI Cloud project started in 2016 as collaboration between the universities of Bielefeld, Freiburg, Gießen, Heidelberg and Tübingen. The close cooperation with the ELIXIR cloud ensures the connectivity and sustainability in the international context. The de.NBI Cloud operates the major service levels: • Infrastructure as a Service (IaaS) suited for experienced power users that want full control over the compute environment; plain access to virtualized infrastructure • Platform as a Service (PaaS) suited for experienced users who utilize fully configured infrastructure for the deployment of custom workflows • Software as a Service (SaaS) suited for users without cloud experience who can use virtual machines (VMs) of pre-configured, state-of-the-art analysis tools and pipelines Cloud computing requires initial efforts and skills to port existing workflows to these new mod-els. The same holds true for emerging programming models. Cloud environments can be difficult to use by scientists with little system administration and programming skills. Challenges exist in managing cloud environments as there is a lack of tools which simplify accessing and using these environments and helping bootstrap users by providing basic software stacks. Keywords: OpenStack, Cloud Computing, virtual machines (VMs) Tools: OpenStack, BiBiGrid Prerequisites: The participants should bring their own laptop computers. The goal of the tutorial is to provide a fundamental introduction to the underlying OpenStack infrastructure. Target audience are bioinformaticians or experienced computational data analysts who would like to utilize scalable and flexible cloud resources for their research. Participants will learn how to setup a cloud project and work with virtual instances, and how to efficiently utilize cloud computing resources. We will also address networking and security issues, demonstrate how to deploy bioinformatics tools in the cloud, and how to set up a customized compute cluster in a cloud environment using BiBiGrid. All topics will be covered by short talks and practical hands-on sessions. 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Introduction to genome-wide association studies (GWAS) 2019

    18 September 2019

    Kiel, Germany

    Introduction to genome-wide association studies (GWAS) 2019 https://tess.elixir-europe.org/events/introduction-to-genome-wide-association-studies-gwas-2019 Educators: David Ellinghaus (Associated partner - CAU) Date: September 18, 2019 Time: 08:30 - 16:30 Location: Kiel, Am Botanischen Garten 1-9, Room E49 This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis. Contents: Over the past decade, genetic epidemiology studies have progressed from studying single genetic variants in candidate genes to investigating millions of common genetic variants in genome-wide association studies (GWAS). Nowadays GWAS studies are moving forward to genome-wide rare variant association studies, gene-gene (GxG) and gene-environment (GxE) interaction studies as well as cross-phenotype studies including several 10k and sometimes even >100k genetic samples. Learning goals: In this one day course we will give guidance for planning of SNP array genotyping and will provide best-practices for large-scale quality control, variant annotation and association analysis of GWAS data. In the practical part of the course will work on real-world data sets and show how to automatically and manually analyze large case-control sample sets and how to annotate phenotype-associated genomic regions. Prerequisites: None Keywords: genome-wide association studies (GWAS); SNP genotype quality control; association testing 2019-09-18 08:00:00 UTC 2019-09-18 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []
  • Eukaryote genome annotation workshop 2019

    19 September 2019

    Kiel, Germany

    Eukaryote genome annotation workshop 2019 https://tess.elixir-europe.org/events/eukaryote-genome-annotation-workshop-2019 Educators: Marc Höppner (Associated partner - CAU) Date: September 19, 2019 - 08:30 - 16:30 Location: Kiel, Am Botanischen Garten 1-9, Room E49 Contents: The constant drop in sequencing prices and the development of easy-to-use assembly programs makes it possible, even for small groups, to embark on a de novo genome project to obtain the full sequence of their species of interest. However, automatically annotating all genetic features in a eukaryotic genome, especially in non-model species with few or no sequenced closely related species, remains a challenge and standard pipelines still do not exist. Learning goals: In this one day course participants will learn about these challenges and the current strategies that can be used to try to obtain the most complete set of genes from a de novo assembled eukaryotic genome. We will also discuss how additional data, such as RNA-seq, assembled transcriptomes or proteomic data, can be used to improve the annotation, which can inform decisions on how best to spend the budget during a genome project. The practical part of the course will explain how to automatically and manually annotate a genomic region and how that information can be immediately translated into biologically relevant data for the species of interest. Prerequisites: None Keywords: eukaryotic genome, annotation, RNAseq proteomic data, assembly Contact: Marc Höppner, m.hoeppner@ikmb.uni-kiel.de This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis. 2019-09-19 09:00:00 UTC 2019-09-19 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []
  • Protein Structure Fundamentals: Searching – Analyzing – Modeling

    23 - 24 September 2019

    Hamburg, Germany

    Protein Structure Fundamentals: Searching – Analyzing – Modeling https://tess.elixir-europe.org/events/protein-structure-fundamentals-searching-analyzing-modeling Educators: Eva Nittinger (BioData), Matthias Rarey (BioData), Ida Schomburg (BioData), Greg Landrum (CIBI) Date: 23./24.09.2019 Location: Universität Hamburg, ZBH – Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg Contents: In this workshop, you will get to know a combination of tools and webservices for searching and analyzing protein structure data. The focus will be on protein function and related interactions to small molecules. We will work with two web- and two software platforms: BRENDA, the database for enzyme structures will be used to gather information about enzyme structures. The ProteinsPlus web service contains a diverse range of software solution for the analysis of protein structures and its application in molecular modeling approaches. NAOMI ChemBio Suite contains desktop software for cheminformatics and advanced modeling. KNIME offers diverse options for the analysis of biological data and the generation of analytical workflows. Learning goals: This course is designed for life and computer scientists with interest in protein structures, but only very basic experience. Topics include: Finding and selecting protein structure data, evaluating the quality of experimental data, preprocessing structure data for modeling, first modeling steps like the analysis of binding site properties and conformational flexibility. Furthermore, we will introduce basic Cheminformatics tools. Usage of ProteinsPlus, BRENDA, NAOMI ChemBio Suite, and KNIME; all software introduced is available for free for academic use. Prerequisites: General knowledge of proteins and their role in life sciences Keywords: Protein structures, protein-ligand interactions, molecular modeling, structure-to-function relationships, cheminformatics, ProteinsPlus, BRENDA, EnzymeStructures, KNIME Tools: ProteinsPlus, BRENDA, NAOMI ChemBio Suite, KNIME 2019-09-23 09:00:00 UTC 2019-09-24 17:00:00 UTC de.NBI Hamburg, Hamburg, Germany Hamburg Hamburg Germany [] [] [] workshops_and_courses [] []
  • 8th Galaxy workshop on HTS data analysis

    23 - 27 September 2019

    Freiburg im Breisgau, Germany

    8th Galaxy workshop on HTS data analysis https://tess.elixir-europe.org/events/8th-galaxy-workshop-on-hts-data-analysis Educators: RBC Freiburg Date: 23.-27.09.2019 Location: Uni Freiburg Contents: 1-week full-day hands-on workshop in Freiburg. Topics: - Galaxy Introduction - Data analysis of RNA-seq, ChIP-seq, Exome-seq, MethylC-seq data Learning goals: Using Galaxy for data analysis of HTS data. Topics: - Quality control - Mapping - Differential expression analysis - Workflow design - Statistics - Visualization. Prerequisites: No. Beginner training course! Keywords: Galaxy, NGS, HTS, RNA-seq, ChIP-seq, Exome-seq, MethylC-seq Tools: Galaxy 2019-09-23 09:00:00 UTC 2019-09-27 17:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany [] [] [] workshops_and_courses [] []
  • de.NBI - CeBiTec Nanopore Best Practice Workshop 2019

    25 - 27 September 2019

    Bielefeld, Germany

    de.NBI - CeBiTec Nanopore Best Practice Workshop 2019 https://tess.elixir-europe.org/events/de-nbi-cebitec-nanopore-best-practice-workshop-2019 de.NBI - CeBiTec Nanopore Best Practice Workshop 2019 Bielefeld Educators: Stefan Albaum, Sebastian Jünemann, Nils Kleinbölting, Alexander Sczyrba (BiGi), Daniel Wibberg (CAU), Björn Usadel (GCBN), Christian Rückert, Jörn Kalinowski (CeBiTec) Date: 25 - 27 September 2019 Location: Bielefeld University, Universitätsstraße 25, 33615 Bielefeld Content: Aim of this workshop is to familiarise the participants with the Nanopore sequencing technology, its applications and the "Best Practice" bioinformatics workflow. The Nanopore technology have greatly facilitated the assembly of prokaryotic and eukaryotic genomes. Therefore, the workshop is focused on the establishment of finalized genome sequences. This workshop will be composed of different talks including introductions to the Nanopore sequencing technology and working in the de.NBI cloud as well as different hands-on sessions. During the talks, the advantages and pitfalls of Nanopore sequencing will be discussed. The hands-on sessions will illustrate the typical workflow from the Nanopore sequencing to the final assembled genome. Learning goals: This workshop aims to teach basic skills and best practices to researchers working with Nanopore data. The final goal is to enable them to use the resulting reads for a de novo assembly. Prerequisites: This workshop is intended for PhD students and postdocs with molecular biology background in genomics. Good understanding of command line tools is a plus, but not required. Tool: Canu, Pilon, Albacore, Porechop, Metricor, Poretools Keywords: Nanopore sequencing, genome assembly, genomics 2019-09-25 09:00:00 UTC 2019-09-27 17:00:00 UTC de.NBI / CeBiTec Bielefeld, Bielefeld, Germany Bielefeld Bielefeld Detmold Germany [] [] [] [] [] []
  • 4th de.NBI Training Course on Metagenome Analysis

    9 - 11 October 2019

    Bielefeld, Germany

    4th de.NBI Training Course on Metagenome Analysis https://tess.elixir-europe.org/events/4th-de-nbi-training-course-on-metagenome-analysis Educators: Sebastian Jünemann (Bielefeld University), Dr. Alex Sczyrba (Bielefeld University), Sebastian Jaenicke (Giessen University), Nils Kleinboelting (Bielefeld University) Location: Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Room V6-113 Date: October the 9th to 11th, 2019 Content: The aim of this 3-day workshop will be to give students a brief overview of the tools and bioinformatics techniques available for the analysis of next generation sequence (NGS) data from microbial communities. The format will comprise a mixture of lectures and hands-on tutorials where students will process example data sets in real-time in the de.NBI cloud environment. After covering general aspects of sequence based analysis (e.g. pre-processing, quality measurements, error handling, and so on) the course is divided into two parts: targeted (16S rRNA gene amplicons) and untargeted (whole-genome shotgun; WGS) metagenome analysis. On demand, a compact introduction into the Linux operating system and the usage of the command line interface will be given upstream to the introducing part to guarantee a consistent baseline for the following lectures. The main aspects of the 16S part are the common pipeline steps beginning with pre-processing and filtering followed by OTU clustering, taxonomic classification, and different statistical measurements. Then, the new ASV/zOTU approach will be introduced followed by similar statistics and both approaches discussed with the attendants in conclusion. In the third part, advantages and disadvantages of whole metagenome sequencing will be illustrated. As WGS metagenomics has the potential to address the full spectra of genome-based issues, the focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools. Two different techniques to analyze WGS metagenome data are part of this section: (1) in the read-based approach the software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated. (2) the assembly-based approach to potentially recover near-complete genome by assembling reads into contigs which are subject to binning methods to group individual contigs into genome bins. Prerequisites: - basic knowledge in microbiology and NGS-based analysis - practical experience in a Linux/Unix derivatives, the command line interface and file system required Prerequisites for the workshop plus the optional Linux introduction: - basic knowledge in microbiology and NGS-based analysis Please not that participation to this course does not depend on the actual Linux experience of the applicant. Both, experienced as well as inexperienced Linux users are encouraged to submit an application. However, the Linux introducing session in the morning of the first day is optional only for applicants fulfilling the Linux prerequisite. Application: Please send your application to denbi-courses@cebitec.uni-bielefeld.de (subject MG­course2019) including a short motivation, a few words about your background, your level of experience on the command line (Linux/Unix), and your experience within the field of metagenomic analysis and related bioinformatic tools. There will be no participation fee, yet travel and accommodation expenses need to be paid by the participants. 2019-10-09 09:00:00 UTC 2019-10-11 17:00:00 UTC de.NBI Bielefeld, Bielefeld, Germany Bielefeld Bielefeld Detmold Germany [] [] [] workshops_and_courses [] metagenomics
  • Software Carpentry Workshop

    16 - 18 October 2019

    Heidelberg, Germany

    Software Carpentry Workshop https://tess.elixir-europe.org/events/software-carpentry-workshop-ab3af408-aa91-49ed-bab2-5db1f2e6d15d Educators: Malvika Sharan, Georg Zeller, Mike Smith, Thomas Schwarzl, Frank Thommen (HD-HuB), Holger Dinkel Date: 16-10-2019 - 18-10-2019 09:00-18:00 Location: ATC Computer Training Lab, EMBL Heidelberg Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2019-10-16 09:00:00 UTC 2019-10-18 17:00:00 UTC de.NBI / ELIXIR Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Introduction to BRENDA and EnzymeStructures

    23 - 24 October 2019

    Braunschweig, Germany

    Introduction to BRENDA and EnzymeStructures https://tess.elixir-europe.org/events/introduction-to-brenda-and-enzymestructures Educators: Antje Chang, Ida Schomburg, Stefan Bietz, Sandra Placzek, Lisa Jeske (BioData) Date: 23.-24.10.2019 Location: TU Braunschweig, BRICS 2019-10-23 09:00:00 UTC 2019-10-24 17:00:00 UTC de.NBI Braunschweig, Braunschweig, Germany Braunschweig Braunschweig Germany [] [] [] workshops_and_courses [] []
  • COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology – ICSB 2019

    31 October 2019

    Japan

    COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology – ICSB 2019 https://tess.elixir-europe.org/events/combine-de-nbi-tutorial-modelling-and-simulation-tools-in-systems-biology-icsb-2019 Educators: Andreas Weidemann, Martin Golebiewski (HITS gGmbH, Heidelberg, Germany), Frank Bergmann, Jürgen Pahle, Sven Sahle (University of Heidelberg, Germany) (de.NBI-SysBio) in collaboration with educators from UK, New Zealand, Japan, Germany, USA Date: Thursday, October 31st, 2019 Links: http://co.mbine.org/events/tutorial2019 Location: Okinawa Insitute of Science and Technology Graduate University Okinawa, Japan Contents: This tutorial workshop is a satellite of the 20th International Conference on Systems Biology (ICSB). Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats and how they support reproducible and FAIR computational modelling. The topics covered will include: - Reproducibility and FAIR (Findable, Accessible, Interoperable and Re-usable) data - Curation services - Model setup using different software tools and systems biology platforms - Using experimental data for setting up quantitative models - Parameter estimation, optimization and model fitting - Simulation, analysis and visualization of biochemical models, and multicellular modelling - Constraint-based and logical modeling of metabolic and signaling networks - Database supported modelling: integrated data management and model databases - Community standards and formats for systems and synthetic biology models - Machine learning for model reduction and image analysis Prerequisites: Laptop Keywords: systems biology, software tools, quantitative models, parameter estimation, model simulation, logical modeling, metabolic networks, model databases, community standards Tools: BioModels, CellDesigner, COPASI, Morpheus, Physiome Model Repository / OpenCOR, SABIO-RK, SEEK/FAIRDOMhub, tellurium, Virtual Cell 2019-10-31 09:00:00 UTC 2019-10-31 17:00:00 UTC de.NBI Präfektur Okinawa, Japan Präfektur Okinawa Japan [] [] [] workshops_and_courses [] []
  • Lipidomics MS Data processing, identification & quantification - Lipidomics Forum 2019

    10 November 2019

    Borstel, Germany

    Lipidomics MS Data processing, identification & quantification - Lipidomics Forum 2019 https://tess.elixir-europe.org/events/lipidomics-ms-data-processing-identification-quantification-lipidomics-forum-2019 Educators: Jacobo Miranda Ackermann, Nils Hoffmann (BioInfra.Prot / LIFS) Date: November 10th, 2019 Location: Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019) Contents: In this course, we will work through a typical use-case for bioinformatics processing lipidomics data following MS acquisition. The first part of the course will start with PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The second part of the course will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to a provided data set. 10:00 - 10:45 Common Introduction 10:45 - 12:30 LipidXplorer Shotgun Lipidomics 12:30 - 13:30 Lunch break 13:30 - 16:30 LipidCreator & Skyline Targeted LC-MS lipidomics Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Participants are required to bring their own laptop in order to work on the hands-on exercises. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline 2019-11-10 09:00:00 UTC 2019-11-10 17:00:00 UTC de.NBI Borstel, Borstel, Germany Borstel Borstel Germany [] [] [] [] [] []
  • Statistical analysis & qualitative and quantitative comparison of lipidomics data - Lipidomics Forum 2019

    10 November 2019

    Borstel, Germany

    Statistical analysis & qualitative and quantitative comparison of lipidomics data - Lipidomics Forum 2019 https://tess.elixir-europe.org/events/statistical-analysis-qualitative-and-quantitative-comparison-of-lipidomics-data-lipidomics-forum-2019 Educators: Fadi al Machot, Nils Hoffmann (BioInfra.Prot / LIFS) Date: November 10th, 2019 Location: Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019) Contents: In this course, we will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards. We will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology, before finally comparing and visualizing our quantitative lipidome results with ClovR. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. 10:00 - 10:45 Common Introduction 10:45 - 12:30 R Scripting for LipidXplorer data quantification Quantitative lipidome comparison wiht ClovR 12:30 - 13:30 Lunch break 13:30 - 16:30 Qualitative lipidome with LUX Score Machine learning, clustering and classification for lipidomics data Learning goals: Participants will be able to understand and explain the shotgun lipidomics data analysis workflow. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based applications. Basic knowledge of R and RStudio is a plus to understand the quantitation workflow. Participants are required to bring their own laptop in order to work on the hands-on exercises. Keywords: Lipidomics, Statistical Analysis, Visualization Tools: R, RStudio, LUX Score, ClovR. 2019-11-10 09:00:00 UTC 2019-11-10 17:00:00 UTC de.NBI Borstel, Borstel, Germany Borstel Borstel Germany [] [] [] workshops_and_courses [] []
Note, this map only displays events that have geolocation information in TeSS.
For the complete list of events in TeSS, click the grid tab.