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Veranstaltungen

Next-Generation Sequencing Data Analysis: A Practical Introduction [December 12-14, 2022]

In a Nutshell:
- Learn the essential computing skills for NGS bioinformatics
- Understand NGS technology, algorithms and data formats
- Use bioinformatics tools for handling sequencing data
- Perform first downstream analyses and find differentially expressed genes

Scope and Topics:
The purpose of this workshop is to get a deeper understanding in
Next-Generation Sequencing (NGS) with a special focus on bioinformatics
issues. Advantages and disadvantages of current sequencing technologies
and their implications on data analysis will be discovered. The
participants will be trained on understanding their own NGS data,
finding potential problems/errors therein and finally perform their
first downstream analysis (differential gene expression). In the course
we will use a real-life RNA-seq dataset from the current market leader
illumina.
All workshop attendees will be enabled to perform important first tasks
of NGS data analysis themselves. The course layout has been adapted to
the needs of beginners in the field of NGS bioinformatics and allows
scientists with no or little background in computer science to get a
first hands-on experience in this new and fast evolving research topic.

Novel challenges in the quest for orthologs [17. - 18. Sept. 2022]

Orthologs are evolutionarily related genes in different species whose separation from the same ancestral sequence was initiated by a speciation event. The identification of orthologs is fundamental for biological sequence analysis both in an evolutionary and functional context. For the bioinformatics community, the quest for orthologs poses a rich source of challenges ranging from the development of scalable algorithms for ortholog classification to the hosting of dedicated data repositories to disseminate orthology assignments into a global community. As such, the development and improvement of orthology inference tools has to keep up with the evolution in the underlying data with respect to both quantity and quality. Some of the currently most pressing challenges are the following. The Darwin Tree of Life project alone will sequence over 70,000 eukaryotic genomes over the next several years. This data is invaluable for biodiversity genomics, but renders the development of orthology inference methods that scale to this wealth of data an urgent task. In the same way as the taxonomic breadth of sequenced organisms increases, deep orthology relationships between genes in distantly related species or between rapidly evolving sequences move into focus. Here, novel algorithms that incorporate information provided by the increasing availability of accurate protein structure predictions may help. The functional diversity and relevance of non-coding RNAs in the regulatory network of a cell, which emerged in the past decade, requires dedicated tools whose standards meet those achieved for protein coding genes. Eventually, the focus beyond cellular organisms is necessary given the spread of pathogenic viruses worldwide. Viral genes diverge quickly and often their evolutionary history is reticulated due to frequent recombination and horizontal gene transfer. Overlapping genes and polyprotein further complicate the identification of orthologous groups. This workshop aims at highlighting these novel challenges in the quest for orthologs for which innovative bioinformatics solutions are urgently needed. The workshop goal is to communicate these topics to, and to discuss possible approaches with a diverse bioinformatics community. This will significantly broaden the methodological basis from which future approaches of orthology inference can be built on and fosters the formation of new collaborations that will significantly advance the field of orthology inference.

Links: https://tinyurl.com/5n6m2t4v

International Symposium on Image-based Systems Biology [ 8. bis 9. September 2022]

Researchers from all fields are invited to communicate their results centered on Image-based Systems Biology in order to exchange novel scientific methods and to share recent achievements from image-driven research in biology. Joint studies of experiment and theory will be highly welcomed. Furthermore, demonstrations of methods for accurate segmentation and classification of regions of interest or object-tracking that can be applied for high-content and high-throughput screening are of interest, as well as computational methods for translating images into mathematical models ranging from differential equations to agent-based methods.

The International Symposium on Image-based Systems Biology has taken place biannually since 2012 at the HKI-Center for Systems Biology of Infection in Jena, Germany.

Link: https://asb-conference.hki-jena.de/

International Symposium on Image-based Systems Biology [8. - 9. September 2022]

Researchers from all fields are invited to communicate their results centered on Image-based Systems Biology in order to exchange novel scientific methods and to share recent achievements from image-driven research in biology. Joint studies of experiment and theory will be highly welcomed. Furthermore, demonstrations of methods for accurate segmentation and classification of regions of interest or object-tracking that can be applied for high-content and high-throughput screening are of interest, as well as computational methods for translating images into mathematical modelsranging from differential equations to agent-based methods.

The International Symposium on Image-based Systems Biology has taken place biannually since 2012 at the HKI-Center for Systems Biology of Infection in Jena, Germany.

Link: https://asb-conference.hki-jena.de/

Women in Bioinformatics: Prof. Dr. Nadine Ziemert, 18.05.21, 12:30

Are you interested in a scientific career as a woman in bioinformatics? But you have questions and worries regarding how to get there?

The online lecture series "Women in Bioinformatics" provides the answers. Successful female scientists present their research, their career path and answer your questions.

The series continues with

Prof. Dr. Nadine Ziemert

on 18.05.21 at 12:30-14:00.

Prof. Ziemert is professor for Natural Product Genome Mining at the University of Tübingen. Her work focuses on developing bioinformatic tools for the discovery of natural products from microbial genomes, elucidating the evolutionary history of their biosynthetic gene clusters and tracing their distribution in the environment.

Participation is free but registration is required for every talk. Registration starts 6 weeks before each talk.

Details and registration: https://www.bio.ifi.lmu.de/wib

Schedule:

27.04.21          12:30-14:00    Prof. Dr. Ina Koch

18.05.21          12:30-14:00    Prof. Dr. Nadine Ziemert

08.06.21          17:00-18:30    Prof. Dr. Kay Nieselt

29.06.21          16:00-17:30    Prof. Dr. Birte Kehr

20.07.21          12:30-14:00    Prof. Dr. Sabine Fischer

For further updates register for our Newsletter: https://lists.lrz.de/mailman/listinfo/wbioinformatics

Follow us on Twitter: https://twitter.com/WBioinformatics

 

 

5th Berlin Summer School 2021

  • Learn the essential computing skills for NGS bioinformatics
  • Understand NGS analysis algorithms (e.g. read alignment) and data formats
  • Use bioinformatics tools for handling NGS data
  • Perform first downstream analyses for studying genetic variation
  • Compare different approaches for differential expression analysis

The purpose of this intense one week summer course is to get a deep understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. You will be trained on understanding NGS data formats and handling potential problems/errors therein. In the summer school we will use a real-life RNA-seq dataset from the current market leader illumina.

All students will be enabled to perform important first tasks of NGS data analysis themselves. The layout of the summer school has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.

In the evenings there will be social events, like a conference dinner, or a guided city tour through Berlin. These are always great networking possibilities.

Link: https://www.ecseq.com/workshops/workshop_2021-01-5th-Berlin-Summer-School-NGS-Data-Analysis

Bioinformatics Pipeline Development with Nextflow [May 3-6, 2021]

Streamline your research through the development of reproducible analysis pipelines

In a nutshell

  • Learn the fundamental best-practices of bioinformatic pipeline development
  • Understand how workflow management systems can accelerate your research
  • Use state-of-the-art, open source software to make complex analyses routine
  • Perform your own custom analysis pipelines using Nextflow

The purpose of the workshop is to introduce the concepts of bioinformatic pipeline development through the context of the open source Workflow Management System (WMS) Nextflow. The participants will be trained in the scripting, configuration and execution of example analysis pipelines based on current industry best-practices, and learn how to share them with other users. Finally, the participants will apply everything they have learned by implementing their own analysis pipelines from the ground up.

By the end of the workshop all attendees will be enabled to build their own scalable, reproducible bioinformatic pipelines which can be run locally, on high-performance computing clusters or even in the cloud. The course layout has been adapted to the needs of beginners in the field of computational biology and allows scientists with little or no background in software development to get a first hands-on experience in this new and fast-evolving area of expertise. This instructor-led live online workshop has been newly designed for an engaging, interactive online learning experience.

DNA Methylation Data Analysis Workshop [April 12-15, 2021]

Advance your epigenetics research with NGS methods.

In a nutshell

  • Learn how bisulfite sequencing works
  • Understand how bisulfite-treated reads are mapped to a reference genome
  • Perform basic analyses (call methylated regions, perform basic downstream analyses)
  • Use shell scripting to create reusable data pipelines
  • Visualize results (ready-to-publish)

The purpose of this workshop is to get a deeper understanding of the use of bisulfite-treated DNA in order to analyze the epigenetic layer of DNA methylation. Advantages and disadvantages of the so-called 'bisulfite sequencing' and its implications on data analyses will be covered. The participants will be trained to understand bisulfite-treated NGS data, to detect potential problems/errors and finally to implement their own pipelines. After this course they will be able to analyze DNA methylation and create ready-to-publish graphics.

By the end of this workshop the participants will:

  • be familiar with the sequencing method of Illumina
  • understand how bisulfite sequencing works
  • be aware of the mapping problem of bisulfite-treated data
  • understand how bisulfite-treated reads are mapped to a reference genome
  • be familiar with common data formats and standards
  • know relevant tools for data processing
  • automate tasks with shell scripting to create reusable data pipelines
  • perform basic analyses (call methylated regions, perform basic downstream analyses)
  • plot and visualize results (ready-to-publish)
  • be able to reuse all analyses

Link: https://www.ecseq.com/workshops/workshop_2021-04-NGS-DNA-Methylation-Data-Analysis

Online Course - A Practical Introduction to NGS Data Analysis [March 1-3, 2021]

Advance your research. Understand NGS and analyze sequenced data yourself.
In a nutshell

  •     Learn the essential computing skills for NGS bioinformatics
  •     Understand NGS technology, algorithms and data formats
  •     Use bioinformatics tools for handling sequencing data
  •     Perform first downstream analyses for studying genetic variation

The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this fast evolving research topic.

The online course will make use of a web conferencing system. Hands-on NGS analysis will be performed in an interactive browser-based data analysis platform. Before the course, you will get a printed manuscript.

 



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