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117 events found

Organizer: Cardiff University  or de.NBI 

  • An Introduction to ChIP-seq Data Analysis

    16 July 2019

    Hamburg, Germany

    An Introduction to ChIP-seq Data Analysis https://tess.elixir-europe.org/events/an-introduction-to-chip-seq-data-analysis Educators: Malik Alawi (UKE), Ceren Saygi (UKE) (External Partner) Date: 16th July 2019 Location: Center for Bioinformatics Hamburg, Bundesstrasse 43, 20146 Hamburg, Room 18 Contents: - Short introduction to ChIP and sequencing - Quality assessment and control of sequence reads - Aligning reads to a reference assembly (mapping) - Peak calling - Associating peaks with genes and other genomic features (peak annotation) - Visualization - Motif detection Learning goals: Hands-on exercises performed during this one-day workshop will enable participants to perform ChIP-seq data analyses on the Linux command line. Prerequisites: A basic understanding of the Linux command line and the (biological) ChIP-seq method are required to attend this course. Keywords: Chip-seq, Chipseq Tools: Fastqc, trimmomatic, bowtie, macs2, homer, igv 2019-07-16 09:00:00 UTC 2019-07-16 17:00:00 UTC de.NBI Hamburg, Hamburg, Germany Hamburg Hamburg Germany [] [] [] workshops_and_courses [] []
  • 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 [] []
  • Tools for reproducible research - ISMB/ECCB 2019

    21 July 2019

    Basel, Switzerland

    Tools for reproducible research - ISMB/ECCB 2019 https://tess.elixir-europe.org/events/tools-for-reproducible-research-0ed30b48-9c67-48f5-8616-6ca21c78c509 Educators: Bjoern Grüning (RBC), Johannes Köster, Devon Ryan Date: 21.07.2019 Location: ISMB/ECCB Basel Content: The typical data analyst must simultaneously juggle multiple projects, each having its own duration and software requirements. As few analysts have any formal training on structuring or even writing the code necessary to perform an analysis, it is unsurprising that the iterative analytic process can produce a wide assortment of almost identically named files (e.g., “final_results.txt”, “final_results.version2.txt”, “final_results.really_final.txt”), all with unclear origins and produced with a hodge-podge of similarly poorly named scripts. The near impossibility of tracing a results file to the exact process that produced it creates untold difficulties both when it comes time to publish results as well as when planning subsequent experiments months or years later (afterall, which of the “final_results” files was really the “right one”?). These issues are further compounded by software paths and other similar assumptions being hard-coded into scripts, preventing easy analysis replication elsewhere. Performing analyses in a reproducible and traceable manner is clearly needed to combat such problems. Schedule Overview 2:00 - 2:10 pm Installing conda and snakeMake 2:10 - 2:30 pm Intro to conda and bioconda (slides) 2:30 - 3:30 pm Hands-on Session: creating conda envs and installing packages from bioconda repo This practical would require installing hisat, samtools and deeptools via bioconda 3:30 - 4:00 pm Hands-on Session: writing conda recipes Topics in BioVis (including examples) Visualization of sequences, macromolecules, omics data, biological networks 4:00 - 4:15 am Coffee Break 4:15 - 4:35 pm Intro to snakemake Specific tools for visualizing large-scale biological data 4:35 - 6:00 Hands On Session: Writing a snakemake workflow wrapper for mapping, indexing and creating coverage files Learning goals: In this hands-on tutorial, we demonstrate how Conda can be used to deploy specific software versions easily, reproducibly, and without administrator credentials. Moreover, we demonstrate how Conda’s ability to create isolated software environments helps to avoid side-effects between different analyses or different steps of the same analysis. Attendees will also learn how to create conda recipes themselves, so they can contribute new packages to projects such as Bioconda. We further demonstrate how Snakemake can be used in combination with Conda and Containers to create reproducible analysis workflows and execute them on any platform from workstations to clusters and the cloud. Finally, using snakePipes as an example, we demonstrate how Conda and Snakemake can be used to define reproducible and flexible workflows for complex genomics analysis. Prerequisites: - Laptops with Linux or MacOS - Pre-installed Miniconda - install via miniconda : https://conda.io/miniconda.html - Expected audience should have basic familiarity with python, git and the command line. Keywords: Conda, Bioconda, snakemake, Bioconductor, reproducible research Tools: Conda, Bioconda, snakemake, 2019-07-21 09:00:00 UTC 2019-07-21 17:00:00 UTC de.NBI Basel, Basel, Switzerland Basel Basel Basel-Stadt Switzerland [] [] [] meetings_and_conferences [] []
  • 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 [] []
  • RNA-Seq data analysis with Galaxy for clinical applications - GMDS 2019

    8 September 2019

    Dortmund, Germany

    RNA-Seq data analysis with Galaxy for clinical applications - GMDS 2019 https://tess.elixir-europe.org/events/rna-seq-data-analysis-with-galaxy-for-clinical-applications-gmds-2019 Educators: Andrea Bagnacani, Markus Wolfien (RBC / de.STAIR) Location: Emil-Figge-Straße 44, 44227 Dortmund Date: 08.09.2019, 10:00 - 18:00 Contents: In this workshop, we provide a summary of the applications of Next Generation Sequencing (NGS) technologies in the clinical context. These are presented through a hands-on session on RNA-Seq data analysis, following a use case to tudy a clinical NGS dataset. Leveraging on the Galaxy environment, we guide the participants through all relevant steps for carrying out the analysis, as well as linking the obtained results with current gene-disease-related databases, or other relevant resources to highlight the clinical impact of the technology. Finally, we discuss our audience's NGS experiments, and provide advice on their NGS data analysis approaches. Learning goals: Get familiar with the Galaxy framework (https://usegalaxy.eu) for carrying out scientific data analyses, learn methods for data exploration and quality control of NGS datasets, and get familiar with the concepts underlying genome alignment and data visualization of subsequent results. Prerequisites: This workshop is intended for MSc/PhD students, postdocs, and researchers with a background in Life Science research. Keywords: Galaxy, Reproducibility, Workflow development, RNA-Seq data analysis, Visualization Tools: Galaxy (https://usegalaxy.eu), Galaxy Training material (https://galaxyproject.github.io/training-material/) Contact: info@gmds.de Registration: https://gmds.de 2019-09-08 09:00:00 UTC 2019-09-08 17:00:00 UTC de.NBI Dortmund, Dortmund, Germany Dortmund Dortmund Arnsberg 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 Educators: Björn Grüning (RBC), Wolfgang Müller (de.NBI-SysBio) Date: 16.09.2019 Location: Marsilius-Arkaden Turm West, Room K13 Im Neuenheimer Feld **6.130.3** 69120 Heidelberg Germany Contents: There is a huge call towards FAIR data. However, what is *FAIR*? Many of us know how that FAIR means Findable, Accessible, Interoperable, Reusable. However the questions "How do I achieve FAIR?" and "How FAIR is FAIR enough?" are still open to debate. A completely different discussion is: How do I approach making my data FAIR? Making data FAIR can be tedious, manual work. Within this workshop we will demonstrate another approach, i.e. using the workflow system Galaxy, as well as Jupyter Notebooks to extract, enrich, process, and finally upload data into the FAIRDOMHub. This is built around the example use case of building an age estimator for humans from RNA data. On the way, we will give reference to the software and services we provide and the type of advice that we can give. Keywords: FAIR data, Galaxy, Jupyter Notebooks, FAIRDOMHub Tools: Galaxy, Jupyter Notebooks, FAIRDOMHub Prerequisites: None 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 [] []
  • MOFA Workshop - GCB 2019

    16 September 2019

    Heidelberg, Germany

    MOFA Workshop - GCB 2019 https://tess.elixir-europe.org/events/mofa-workshop-gcb-2019 Educators: Oliver Stegle (HD-HuB) Date: 16.09.2019 Location: Heidelberg, Germany Contents: This tutorial provides an introduction to Multi-Omics Factor Analysis (MOFA), a novel unsupervised framework for the integration of multi-omic data sets (Argelaguet et al, Molecular Systems Biology. 2018). Intuitively, MOFA can be viewed as a versatile and statistically rigorous generalization of principal component analysis to multi-omics data. Given multiple ‘omics data types on overlapping sets of samples, MOFA infers a low-dimensional data representation in terms of (hidden) factors. These learnt factors represent the driving sources of variation across data modalities, thus facilitating the identification of molecular phenotypes and disease subgroups. In the first part of the tutorial I will give a 30-minute presentation to explain the model, its applications and limitations. The second part will consist on a hands-on activity where we will use two real-case data sets to show how MOFA can be used for integrative analysis. The first data set will be a large study of blood cancer patients (Dietrich, J Clin Invest. 2018), and the second will be a single-cell multi-omics data set (Angermueller, Nature Methods. 2016). The attendants are also encouraged to bring their own multi-omics data sets. Keywords: MOFA, R, Tools: MOFA, R, Prerequisites: A working knowledge of R is expected. The tutorial requires the installation of the following software: • R>=3.4 + Rstudio • Python>=2.7 • MOFA R package (+ dependencies) • MOFAdata R package (+ dependencies) • mofapy python package (+ dependencies) 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 [] []
  • Proteomics and metabolomics with OpenMS and pyOpenMS - GCB2019

    16 September 2019

    Heidelberg, Germany

    Proteomics and metabolomics with OpenMS and pyOpenMS - GCB2019 https://tess.elixir-europe.org/events/proteomics-and-metabolomics-with-openms-and-pyopenms Educators: Julianus Pfeuffer, Timo Sachsenberg Date: 16.09.2019 Location: GCB 2019. Heidelberg Contents: Computational mass spectrometry provides important tools and bioinformatic solutions for the analysis of proteomics data. Different methods for label-free quantification have been developed in recent years and were successfully applied in a wide range of studies. Targeted approaches for label-free quantification, like SWATH-MS, achieve deep proteome coverage over a large number of samples while non-targeted methods have shown great potential in unbiased discovery studies. This de.NBI training event introduces key concepts of both targeted SWATH-MS and non-targeted label-free analysis using workflow-based processing of real-life datasets. We will introduce several open-source software tools for proteomics, primarily focusing on OpenMS (http://www.OpenMS.org). In a hands-on session, we will demonstrate how to combine these tools into complex data analysis workflows including visualization of the results. Participants will have the opportunity to bring their own data and design custom analysis workflows together with instructors. For participants interested in developing their own algorithms and methods within the OpenMS framework, we provide a brief introduction to pyOpenMS – the python interface to the OpenMS development library. Training material and handouts will be prepared for both users that want to design proteomic workflows, as well as training material for algorithm and tool developers. Software Requirements: The participants should bring their own laptop computers. Installer versions of required software will be made available. Keywords: LC-MS based proteomics, OpenMS, workflows, KNIME, data analysis Tools: OpenMS/pyOpenMS, KNIME 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 [] []
  • Integrating computational meta-omics for microbiome research - GCB 2019

    16 September 2019

    Heidelberg, Germany

    Integrating computational meta-omics for microbiome research - GCB 2019 https://tess.elixir-europe.org/events/integrating-computational-meta-omics-for-microbiome-research-gcb-2019 Educators: Dirk Benndorf (BiGi / MetaProtServ), Thilo Muth Date: 16.09.2019 Location: German Cancer Research Center Im Neuenheimer Feld 280 69120 Heidelberg Germany Contents: The field of microbiome research starts to investigate microbial functions in relation to dysbiosis (i.e. the unbalanced composition of the microbiome) being associated with health disorders and disease states. While many microbiome studies mainly rely on genome-based analyses, the integration of meta-omics data at the gene, transcript, protein and metabolite level is a holistic approach that extends the capabilities of microbiome studies. However, the potential of integrative meta-omics has not been fully exploited so far. An important reason is that bioinformatics methods are developed by different research communities. This limits the exchange of ideas and transfer of methods between researchers across different omics fields. In this workshop, we want to bring together bioinformaticians and researchers working in meta-omics and microbiome-focused disciplines. The meta-omics workshop aims to: (i) provide a platform of presenting new algorithms and software tools for integrative multi-omics approaches or related single omics technology (ii) stimulate discussions on challenges and open questions (iii) help exchanging ideas on bioinformatics methods (iv) identify what is currently lacking for integrative omics in microbiome research Abstract proposals for oral presentations (15 min talk + 5 min discussion) of tools, methods or open problems can be submitted until July 31, 2019 Draft schedule: • Abstract deadline for open speaker slots: July 31, 2019 • Response to applications for speaker slots: August 20, 2019 • Each talk is limited to 15 minutes and additional 5 minutes of discussion for each talk. Coffee break of 15 minutes after the first half of the workshop. Final plenary discussion (20 minutes). • Proposed time schedule: 13.30 – 16.30 Learning goals: In this workshop, we want to bring together bioinformaticians and researchers working in meta-omics and microbiome-focused disciplines. Prerequisites: Registration on GCB 2019. Abstract proposals for oral presentations (15 min talk + 5 min discussion) of tools, methods or open problems can be submitted until July 31, 2019 Keywords: Microbiome, Metaproteomics, MetaProteomeAnalyzer, Prophane Tools: MetaProteomeAnalyzer, Prophane Contact: Dr. Thilo Muth (Bioinformatics Unit, Robert Koch Institute, Berlin; mutht@rki.de) Dr. Dirk Benndorf (Bioprocess Engineering, Otto von Guericke University, Magdeburg; benndorf@mpi-magdeburg.mpg.de) 2019-09-16 13:00:00 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 [] []
  • Microscopy Image Analysis Course

    19 - 20 September 2019

    Heidelberg, Germany

    Microscopy Image Analysis Course https://tess.elixir-europe.org/events/microscopy-image-analysis-course Educators: Karl Rohr, Thomas Wollmann, Manuel Gunkel (HD-HuB), Qi Gao, Leonid Kostrykin Date: 19.-20.9.2019 Location: Heidelberg University IPMB (Institute of Pharmacy and Molecular Biotechnology) Im Neuenheimer Feld 364 Contents: The course gives an introduction into the field of microscopy image analysis for cell biology and the use of software tools for automated processing of image data. Basic methods for computer-based analysis of microscopy images are introduced such as image preprocessing, segmentation, feature extraction, classification, colocalization, and tracking. Concepts of software platforms with focus on ImageJ and their use for analyzing cell microscopy image data are also taught. Workflow systems for automating image analysis pipelines are also considered (e.g., KNIME, Galaxy). The course consists of lectures and practical sessions. Participants should bring their laptops for the practical sessions. The target group are researchers with a background in biology or medicine that need to analyze their data and have little or no experience in automated image analysis. Learning goals: - Introduction into cell microscopy image analysis - Application of software tools for automated analysis of image data Prerequisites: Basic knowledge in using software tools for image analysis is helpful but not mandatory Keywords: Computer-based image analysis, image preprocessing, segmentation, feature extraction, classification, colocalization, tracking Tools: Image J Course fee: Participants will be charged with a course fee of 40 Euros (to cover the lunch and infrastructure related cost). The invoice details will be shared via email. Registration: Please register directly on the HD-HuB website: https://www.hd-hub.de/course-dates/3-all/47-microscopy-image-analysis-course In the "Comments" section of the registration form, please provide some information about yourself and your motivation to attend the training (e.g. Position, Field of study/Background, Topic of work, Knowledge of image analysis methods/tools). Registration closes on August 11, 2019. The capacity is limited to 20 participants and applicants will be selected after registration closed. You will be notified of the outcome by e-mail on August 23, 2019. 2019-09-19 09:00:00 UTC 2019-09-20 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] [] [] []
  • 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 [] []
  • RNA-seq workshop for beginners: from sequences to visualization using Galaxy and R

    7 - 9 October 2019

    Rotterdam, Netherlands

    RNA-seq workshop for beginners: from sequences to visualization using Galaxy and R https://tess.elixir-europe.org/events/rna-seq-workshop-for-beginners-from-sequences-to-visualization-using-galaxy-and-r Educators: Bérénice Batut, Helena Rasche (RBC), Saskia Hiltemann, Mateusz Kuzak, Fotis Psomopoulos Date: 07-09.10.2019 Location: Rotterdam, Thessaloniki, Tartu, Contents: Galaxy introduction and RNA-seq Learning goals: - Use Galaxy for data analysis - Control the quality of sequencing data - Map data to a reference genome - Analyze RNA-seq data using a reference genome - Learn basics of R programming Prerequisites: None (Beginner Course) Keywords: Galaxy, Mapping, Quality control, RNA-seq, R, Rstudio Tools: Galaxy, R, Rstudio 2019-10-07 09:00:00 UTC 2019-10-09 17:00:00 UTC de.NBI Rotterdam, Rotterdam, Netherlands Rotterdam Rotterdam Regierung von Rotterdam Netherlands [] [] [] workshops_and_courses [] []
  • 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
  • Galaxy for linking bisulfite sequencing with RNA sequencing

    9 - 12 October 2019

    Freiburg im Breisgau, Germany

    Galaxy for linking bisulfite sequencing with RNA sequencing https://tess.elixir-europe.org/events/galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing-7b7b1d40-b65b-4694-a5c7-9613dfb3e2c7 Educators: Konstantin Riege (Jena), Steve Hoffmann (Jena), Steffen C. Lott (Freiburg), Wolfgang Hess (Freiburg), Andrea Bagnacani (Rostock), Markus Wolfien (Rostock), Olaf Wolkenhauer (Rostock) (RBC / de.STAIR) Date: 9.-11.10.2019 Location: Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau Contents: In this training course, we introduce the Galaxy framework (https://usegalaxy.eu) for biomedical data analyses, and showcase its tools for data handling and preprocessing, differential gene expression analysis, bisulfite sequencing analysis, and Oxford Nanopore data exploration and usage. Lectures will be provided on the topics of RNA and Bisulfite sequencing, Epigenetics, and basic statistics, and followed by hands-on sessions. Finally, we showcase a Galaxy Docker installation for customized workflow analysis. Learning goals: - Know your data, and the implications of data preprocessing and quality control - Performing differential gene expression analysis using Galaxy - Performing differential methylation analysis using Galaxy - Handling and analyze Oxford Nanopore sequencing data Prerequisites: This workshop is intended for MSc/PhD students, postdocs, and researchers with a background in Life Science research. During registration, please hand over a poster about a research topic of your choosing. Posters will be presented during our poster session, which you can use to exchange experiences with other participants. Keywords: Galaxy, Workflow development, Differential gene expressionanalysis, differential methylation analysis, Epigenetics, Oxford Nanopore Tools: Galaxy (https://usegalaxy.eu), Galaxy Training material (https://galaxyproject.github.io/training-material/) Contact: destair@leibniz-fli.de Register: https://www.leibniz-fli.de/de/news-events/seminare/news-detailpage/news/denbidestair-training-course-galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing-1/ 2019-10-09 09:00:00 UTC 2019-10-12 00:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany [] destair [at] leibniz-fli.de [] [] [] [] []
  • Metabolomics Data Clinic October 2019

    11 October 2019

    Metabolomics Data Clinic October 2019 https://tess.elixir-europe.org/events/metabolomics-data-clinic-october-2019 Educators: Peters / Neumann / Meier / Treutler (CIBI / MASH) Date: 2019/10/11 @ 10:00 - 11:00 CEST (UMT+2h) Location: Online Meeting (DFNconf service, connection details after registration) Workshop goals: We want to invite to the next edition of our online Metabolomics Data Clinic. The Data Clinic is a web-based video help desk which addresses (not only) beginners in the field of metabolomics and associated data analyses. We want to help people with their first steps in the exciting and multifaceted field of metabolomics, to facilitate the (sometimes) steep learning curve, and raise awareness of advanced data analysis options. In this Metabolomics Data Clinic we will focus in particular on: - Data Sharing and data standards (MetaboLights Data Repository) - Metabolite identification (MassBank, MetFrag, MetFamily) - Other metabolomics-related topics Mode of action: Our Metabolomics Data Clinic is not a webinar, you can rather think of the coffee break during a conference, where oftentimes valuable suggestions are exchanged. We usually won’t have slides, and don’t prepare a lecture. You are interested and have a question? We will try to answer them or tell you who might be the expert to ask. If you mail your questions to denbi-mash@ipb-halle.de a few days before the data clinic we can prepare and improve our response. Looking forward to see you, Yours, The de.NBI Data Clinic Team Prerequisites: None. Keywords: Metabolomics, mass spectrometry, R, Bioconductor, data processing, metabolite annotation, metabolite identification 2019-10-11 10:00:00 UTC 2019-10-11 11:00:00 UTC de.NBI Metabolomics [] [] [] workshops_and_courses [] Metabolomicsmass spectrometryRBioconductorData processingmetabolite annotationmetabolite identification
  • Analyzing and redesigning metabolic networks with CellNetAnalyzer

    15 October 2019

    Valencia, Spain

    Analyzing and redesigning metabolic networks with CellNetAnalyzer https://tess.elixir-europe.org/events/analyzing-and-redesigning-metabolic-networks-with-cellnetanalyzer Date 15.10.2019 Location FOSBE Conference in Valencia http://fosbe2019.ai2.upv.es/workshops/ Educators Steffen Klamt, Philipp Schneider Max Planck Institute for Dynamics of Complex Technical Systems Contact klamt@mpi-magdeburg.mpg.de Duration ca. 3 hours Target audience Students and researchers interested in constraint-based and stoichiometric modeling of metabolic networks. Some basic experiences in constraint-based modeling would be of advantage but is not an absolute requirement. The workshop will focus on the use of the software CellNetAnalyzer. If the participants want to follow the live demonstration or/and take part in the hands-on session, then they should bring their laptops (with MATLAB installed) along. Abstract CellNetAnalyzer (CNA) is a widely used MATLAB package for analyzing biological (metabolic, signaling and regulatory) networks. CNA and supports both command-line based operations as well as a graphical user interface with embedded network visualizations. In the first part of this workshop (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, phase plane analysis, elementary mode analysis, computational (re)design of metabolic networks based on minimal cut sets, and many more. The second part of the tutorial (1,5h) will consist of hands-on exercises with example networks where the participants will learn how to use CellNetAnalyzer in practice. 2019-10-15 09:00:00 UTC 2019-10-15 17:00:00 UTC de.NBI Valencia, Valencia, Spain Valencia Valencia Provinz Valencia Spain [] [] [] 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 [] []
  • Environmental Genomics training course

    23 - 25 October 2019

    Gießen, Germany

    Environmental Genomics training course https://tess.elixir-europe.org/events/environmental-genomics-training-course Educators: Jochen Blom, Oliver Rupp, Oliver Schwengers, Sebastian Jaenicke (BiGi), Stefanie Glaeser Date: 23.10.2019 – 25.10.2019 Location: Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, Room 0024a Contents: Topic of this three-day-workshop will be sequence data analysis including quality control, assembly, genome annotation and comparative genomics with a focus on microbial taxonomy and phylogenomics and as the usage of the BiGi software tools ASA3P, EDGAR, and MGX. The first day will give a comprehensive introduction to the primary data management in sequencing projects. In this part tools for sequence analysis available via the Galaxy-Server of BIGI will be in the focus of the workshop. • Initial quality assessment and quality control of raw sequencing data • Data preparation, filtering and quality trimming • Assembly strategies for different datasets Furthermore, the basic principles of regional and functional annotation will be introduced, and available tools and algorithms for the different annotation steps will be explained. The ASA3P platform for high-throughput parallel genome annotation and its capabilities in antibiotic resistance and virulence factor detection will be presented in detail. • The basic principles of regional and functional annotation • Genome annotation pipelines for single and multiple genomes • High throughput genome annotation using ASA3P The second day will provide an introduction to the role of genotypic methods in prokaryotic taxonomy including the 16S rRNA gene sequence phylogeny and genome sequences in the identification of environmental isolates. It will will also demonstrate the use of genome sequences to explore the functions of those isolates. • The basic role of 16S rRNA gene sequences in Prokaryotic identification in taxonomic and ecology • Concept of the phylogenetic analysis of environmental 16S rRNA gene amplicon datasets (introduction of SilvaNGS) • Current role of genome sequences in species identification Subsequently the EDGAR platform for comparative genomics will be introduced. One main topic will be its use for phylogenetic analyses based on genome similarity indices and the complete core genome of organisms. All features of EDGAR will be introduced in detail. • Genomic subset calculations (core-genome, pan-genome, singleton genes) • Core-genome-based phylogenetic analyses • Core genome based phylogeny ◦ ANI, AAI, GGDC • Statistical analyses (core/pan/singleton development plots) • The public EDGAR database The third day will show solutions for whole genome shotgun metagenomics. mWGS 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. The software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated as comprehensive platform for read-based metagenome analysis. • The basic principles of metagenome analysis • Available pipelines for taxonomic and functional analysis • Statistical features: PCA, PCoA, Rarefaction, … The afternoon of the third day will be kept free for custom data analysis consulting. Participants are encouraged to bring their own data which can be discussed with the bioinformatics experts of the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi). On all three days the program includes extensive hands-on training to allow participants to become familiar with the presented software. Learning goals: Principles of computational sequence analysis, hands-on experience with de.NBI software services Prerequisites: None Keywords: Sequence data analysis, genomics, annotation, comparative genomics, phylogenetic analysis, metagenome analysis Tools: GenDB, ASA3P, EDGAR, MGX 2019-10-23 09:00:00 UTC 2019-10-25 17:00:00 UTC de.NBI Gießen, Gießen, Germany Gießen Gießen Gießen Germany [] [] [] workshops_and_courses [] []
  • 3rd Tool-Training for Proteomics

    28 October 2019

    Bochum, Germany

    3rd Tool-Training for Proteomics https://tess.elixir-europe.org/events/3rd-tool-training-for-proteomics Educators: Michael Kohl, Treesa Sunny, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot) Date: Monday, 2019-10-28 Location: Ruhr University Bochum, 44801 Bochum Contents: In this one day course we will show some of BioInfra.Prot's tools provided by de.NBI, namely “PIA - Protein Inference Algorithms”, “BIONDA – A Free Biomarker Database” and “CalibraCurve”. Besides the tool based sessions we offer a "Proteomics in the Cloud" session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. PIA allows to inspect and combine the results of proteomics search engines. The main focus lays on the integrated inference algorithms for identification and quantification purposes. BIONDA is a free, up-to-date and user-friendly biomarker and biomarker candidate database that facilitates any kind of research on protein biomarkers and the corresponding diseases. CalibraCurve is a tool intended for the generation of calibration curves in the context of MRM (targeted proteomics) experiments. Such calibration curves are necessary for the selection of suitable transitions. Learning goals: Attendees of the course will learn how to use the tools PIA, BIONDA and CalibraCurve effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud. Prerequisites: This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC-MS data are sufficient. Attendees are required to bring their own laptops. If this is not possible or laptops have very low computing capacities, please contact the organizers. Keywords: Proteomics; Data Analysis; Biomarkers; de.NBI Cloud Tools: PIA; BIONDA; CalibraCurve 2019-10-28 09:00:00 UTC 2019-10-28 17:00:00 UTC de.NBI Bochum, Bochum, Germany Bochum Bochum Arnsberg 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 [] []
  • Advanced modeling with COPASI - ICSB 2019

    31 October 2019

    Japan

    Advanced modeling with COPASI - ICSB 2019 https://tess.elixir-europe.org/events/advanced-modeling-with-copasi-icsb-2019 Educators: Sven Sahle (Heidelberg University), Frank Bergmann (Heidelberg University), Stefan Hoops (University of Virginia), Ursula Kummer (Heidelberg University), Pedro Mendes (University of Connecticut), Jürgen Pahle (Heidelberg University), Egils Stalidzans (University of Latvia) (de.NBI-SysBio / de.NBI-ModSim) Date: Thursday, October 31st, 2019 Links: http://denbi-modsim.de/icsb_copasi_2019/ Registration: https://forms.gle/NepBmMjrXmTzuCpy9 Location: Room 3, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan Contents: COPASI is a widely used software tool for creating, simulating and analysing models of biochemical reaction networks. It is open source free software and available for all major operating systems. Its features include deterministic and stochastic simulation, steady state analysis, stoichiometric analysis, optimisation and parameter estimation, time scale analysis, sensitivities and metabolic control analysis, Lyapunov exponents, linear noise approximation, etc. In the workshop we will demonstrate the use of advanced features of COPASI, focusing on parameter estimation and parameter identifiability analysis, and the use of COPASI from scripting languages. For experienced users of the software, we will present an overview of new features added in the latest releases, such as stochastic differential equation models. A special session will demonstrate an optimisation workflow, highlighting how COPASI can be integrated in third party software projects. The developers of COPASI will also be available for the discussion of individual questions from the participants. Prerequisites: Laptop Keywords: systems biology, software tools, quantitative models, parameter estimation, model simulation, metabolic networks, model databases, community standards Tools: COPASI, 2019-10-31 09:00:00 UTC 2019-10-31 17:00:00 UTC de.NBI Präfektur Okinawa, Japan Präfektur Okinawa Japan [] [] [] meetings_and_conferences [] []
  • Protein-RNA cross-linking with RNPxl/OpenMS - SSP2019

    3 November 2019

    Göttingen, Germany

    Protein-RNA cross-linking with RNPxl/OpenMS - SSP2019 https://tess.elixir-europe.org/events/protein-rna-cross-linking-with-rnpxl-openms-ssp2019 Educators: Timo Sachsenberg, Alexander Wulf (CIBI) Date: 03.11.2019 Location: Workshop 9th Symposium on Structural Proteomics Göttingen, Germany Contents: Proteins and RNA form major classes of biomolecules. Protein-RNA complexes are essential for cellular processes like translation or splicing. In Kramer, Sachsenberg et. al, (Nat Methods, 2014) we demonstrated how protein-RNA interactions can be detected and localized at the level of single amino acids with our tool RNPxl. In this training event, we describe our experimental and computational approach to protein-RNA analysis from UV-induced cross-linking experiments. Software Requirements: none Keywords: LC-MS based proteomics, OpenMS, workflows, cross-linking, data analysis Tools: OpenMS 2019-11-03 09:00:00 UTC 2019-11-03 17:00:00 UTC de.NBI Göttingen, Göttingen, Germany Göttingen Göttingen Germany [] [] [] meetings_and_conferences [] []
  • Machine Learning in R

    6 - 7 November 2019

    Heidelberg, Germany

    Machine Learning in R https://tess.elixir-europe.org/events/machine-learning-in-r Date Nov 6 - Nov 7 2019 Location EMBL Heidelberg Tutors and helpers - Dr. Malvika Sharan - Prof Bernd Bischl - Martin Binder - Giuseppe Casalicchio Affiliation: Ludwig-Maximilians-University Munich Course Information This two-day course, on the implementation of Machine Learning in R, using mlr package will be delivered as practical sessions on programming and data analysis. The main goal of mlr is to provide a unified interface for machine learning tasks as classification, regression, cluster analysis and survival analysis in R. Sessions will be driven by many practical exercises and case studies. Before this workshop, participants are expected to review the official material introducing the principle of Machine Learning (see the prerequisite). Course Content This 2-day course will cover hands-on sessions using `mlr` and other relevant packages. Daily schedule - 09:30-12:30 3h morning, 90 min Theory + 90 min Practical - 12:30-13:30 1h Lunchbreak - 13:30-16:30 3h afternoon, 90 min Theory + 90 min Practical - 16:30-17:00 Time for general questions Day 1 Introduction to the concepts and Practical with mlr - Performance Evaluation and Resampling (Metrics, CV, ROC) - Introduction to Boosting Day 2 Introduction to the concepts and Practical with mlr - Tuning and Nested Cross-Validation - Regularization and Feature Selection Prerequisite The course is aimed at advanced R programmers, preferably with some knowledge of statistics and data modeling (See prerequisite materials from Day-1, 2, & 4). In this course, our learners will learn more about machine learning and its application and implementation through the hands-on sessions and use cases. Optional: Discussion-Based Session On The Principle of Machine Learning Anna Kreshuk (EMBL Group Leader) will lead a one-day discussion-based session on 14 October 2019 to address your questions on the prerequisite materials on the principle of Machine Learning. This will also allow you to connect with other participants of this workshop informally, and discuss the materials in smaller groups. Please register for this workshop separately: https://bio-it.embl.de/events/machine-learning-discussion-workshop-2019/. Registration Please register on this page: https://bio-it.embl.de/events/machine-learning-in-r-2019/ Please note that the maximum capacity of this course is 40 participants and registration is required to secure a place. If you have any questions, please contact Malvika Sharan. In your registration, please mention your EMBL group name, or institute's name (e.g. DKFZ, Uni-HD) if you are registering as an external participant. Costs 60,00 EUR Keywords: Machine Learning, R 2019-11-06 09:00:00 UTC 2019-11-07 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] 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 [] [] [] [] [] []

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