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Swiss Institute of Bioinformatics

The SIB Swiss Institute of Bioinformatics is an academic, non-profit foundation recognised of public utility and established in 1998. SIB coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services to the national and international research community.

Swiss Institute of Bioinformatics https://tess.elixir-europe.org/content_providers/swiss-institute-of-bioinformatics The SIB Swiss Institute of Bioinformatics is an academic, non-profit foundation recognised of public utility and established in 1998. SIB coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services to the national and international research community. /system/content_providers/images/000/000/011/original/sib.png?1469458452
Showing 12 materials.
BLAST and multiple sequence alignment (MSA) programs

Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

Keywords: Blast, E learning, Multiple sequence alignment

BLAST and multiple sequence alignment (MSA) programs https://tess.elixir-europe.org/materials/blast-and-multiple-sequence-alignment-msa-programs Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of new data is very useful to the research field through the development of bioinformatics tools and databases that deal with large amount of sequences. Among them, BLAST (Basic Local Alignment Search Tool) and MSA () programs are very efficient for protein or nucleotide sequence similarity search. The present course introduces the main biological databases, alignment tool BLAST and Multiple sequence alignments (MSA) programs, and interpretation of results. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-zone, Swiss-Prot group at the SIB Swiss Institute of Bioinformatics   Blast, E learning, Multiple sequence alignment Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28 2017-10-09
Introduction to 3D-Structure Visualization and Homology Modeling using the Swiss-Model Workspace

The goal of this course is to expose the participants to 3-dimensional structures of proteins. Analysis and visualization software (DeepView) will be used to display, analyze, compare and interpret protein structures. The second part of the course is dedicated to protein structure prediction...

Introduction to 3D-Structure Visualization and Homology Modeling using the Swiss-Model Workspace https://tess.elixir-europe.org/materials/introduction-to-3d-structure-visualization-and-homology-modeling-using-the-swiss-model-workspace The goal of this course is to expose the participants to 3-dimensional structures of proteins. Analysis and visualization software (DeepView) will be used to display, analyze, compare and interpret protein structures. The second part of the course is dedicated to protein structure prediction using the Swiss-Model expert system for homology modeling.
High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Computer science, Bioinformatics, Biology

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences https://tess.elixir-europe.org/materials/high-performance-computing-hpc-in-life-sciences High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used either as the electronic component of a blended training format or as a self-running learning product. Computer science Bioinformatics Biology High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
Vital-IT Infrastructure Usage

How to efficiently use Vital-IT hardware and software infrastructure.

Vital-IT Infrastructure Usage https://tess.elixir-europe.org/materials/vital-it-infrastructure-usage How to efficiently use Vital-IT hardware and software infrastructure.
SPARQL



SPARQL https://tess.elixir-europe.org/materials/sparql 
How to use V-pipe (SARS-CoV-2 data)

How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)

Scientific topics: Workflows, Genetic variation, Virology

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

How to use V-pipe (SARS-CoV-2 data) https://tess.elixir-europe.org/materials/how-to-use-v-pipe-sars-cov-2-data How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data) Workflows Genetic variation Virology coronavirus, NGS bioinformatics, Variant-calling bioinformaticians Biologists, Genomicists, Computer Scientists
High Performance Computing in Life Sciences

No description provided.

High Performance Computing in Life Sciences https://tess.elixir-europe.org/materials/high-performance-computing-in-life-sciences No description provided.
UNIX Fundamentals

This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of...

Keywords: Problem based learning, Programming, Unix

Resource type: e-learning

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals-35adf82d-ae32-449d-9627-43b5d18da8cc This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of the course, participants are expected to be able to: Have some understanding on UNIX systems Navigate through the UNIX filesystem Execute and understand some UNIX process commands Correctly set file permissions Perform basic file management Participants are encouraged to follow the tutorial sections sequentially. The tutorial content is sometimes an oversimplification of the Truth - yes, we know! Due to the diversity of computer systems, we will just assume that participants do have access to a terminal. For help, please contact your IT support - or a good friend!Authors are affiliated to the SIB Swiss Institute of Bioinformatics: Vassilios IoannidisWith some content provided by Frédéric Schütz, Volker Flegel and Heinz StockingerContent integration by Grégoire Rossier and Vassilios Ioannidis Problem based learning, Programming, Unix Bench biologists Clinical Scientists Graduate Students beginner bioinformaticians biocurators 2014-01-13 2017-10-09
R basics

How to learn R basics

R basics https://tess.elixir-europe.org/materials/r-basics How to learn R basics
Cybersecurity Quiz for SIB employees only (internal use)

No description provided.

Cybersecurity Quiz for SIB employees only (internal use) https://tess.elixir-europe.org/materials/test-sib-security-quiz No description provided.
Phylogenetics of animal viral pathogens

Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

Keywords: Animal pathogens, E learning, Phylogenetics

Resource type: ViralZone

Phylogenetics of animal viral pathogens https://tess.elixir-europe.org/materials/phylogenetics-of-animal-viral-pathogens Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases. The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-Zone, Swiss-Prot Group at SIB Swiss Institute of Bioinformatics   Animal pathogens, E learning, Phylogenetics Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28 2017-10-09
UNIX Fundamentals

This tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience.

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals This tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. 2014-01-13
Showing 20 upcoming events. Found 182 past events. View all results.

  • First steps in Python, and more!

    9 - 11 June 2020

    Basel, Switzerland

    Elixir node event
    First steps in Python, and more! https://tess.elixir-europe.org/events/first-steps-in-python-and-more Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-06-09 09:00:00 UTC 2020-06-11 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First steps with R in Life Sciences - streamed

    3 - 4 June 2020

    Streamed from Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences - streamed https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-4ddd6df7-e4ed-4f77-a73f-8540aae27887 This course will be streamed, and accessible only for the registered participants. The course is now full with a waiting list. Application is now closed. There will be other sessions next year. Thank you for your understanding. 2020-06-03 09:00:00 UTC 2020-06-04 00:00:00 UTC SIB, Streamed from Lausanne, Switzerland SIB Streamed from Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Comparative Genomics

    16 - 18 September 2020

    Lausanne, Switzerland

    Elixir node event
    Comparative Genomics https://tess.elixir-europe.org/events/comparative-genomics-081ccefb-bceb-4008-b66a-ab370648018c Overview The aims of this course are to (i) explore key evolutionary concepts, (ii) examine different methodological approaches, and (iii) gain hands-on experience in eukaryotic comparative genomic analyses. 2020-09-16 09:00:00 UTC 2020-09-18 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • UNIX scripting for Life Scientists

    1 - 2 October 2020

    Lausanne, Switzerland

    Elixir node event
    UNIX scripting for Life Scientists https://tess.elixir-europe.org/events/unix-scripting-for-life-scientists More information on due time... 2020-10-01 09:00:00 UTC 2020-10-02 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First steps with R in Life Sciences

    27 - 28 October 2020

    Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-009cd52b-e152-423a-8888-02c096d98fc5 Overview R is a complete, flexible and open source system for statistical analysis and graphics, which has become a tool of choice for biologists and biomedical scientists who need to analyse and visualise large amounts of data. 2020-10-27 09:00:00 UTC 2020-10-28 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • UNIX scripting for Life Scientists

    1 - 2 October 2020

    Lausanne, Switzerland

    Elixir node event
    UNIX scripting for Life Scientists https://tess.elixir-europe.org/events/unix-scripting-for-life-scientists-ef67aec8-cc7b-4010-8668-fe9d5ba9091d More information on due time... 2020-10-01 09:00:00 UTC 2020-10-02 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First Steps with Perl in Life Sciences (To be confirmed)

    24 - 25 June 2020

    Lausanne, Switzerland

    Elixir node event
    First Steps with Perl in Life Sciences (To be confirmed) https://tess.elixir-europe.org/events/first-steps-with-perl-in-life-sciences SIB has taken the decision to postpone or stream its courses to help slowing down the transmission of the COVID-19. Each course has its own nature, content, delivering mode, learning objectives and complexity. 2020-06-24 09:00:00 UTC 2020-06-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • neXtProt - an introduction

    24 September 2020

    Geneva, Switzerland

    Elixir node event
    neXtProt - an introduction https://tess.elixir-europe.org/events/nextprot-an-introduction-1bbf83e0-213b-4c2e-8a7e-a10424c47354 More information soon 2020-09-24 09:00:00 UTC 2020-09-24 00:00:00 UTC SIB, Geneva, Switzerland SIB Geneva Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First Steps with Python in Life Sciences

    1 - 3 December 2020

    Lausanne, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences More information on due time... 2020-12-01 09:00:00 UTC 2020-12-03 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First Steps with Python in Life Sciences

    1 - 3 September 2020

    Lausanne, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences-date-to-be-confirmed More information on due time... 2020-09-01 09:00:00 UTC 2020-09-03 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Advanced Statistics: Statistical Modeling

    17 - 20 August 2020

    Lausanne, Switzerland

    Elixir node event
    Advanced Statistics: Statistical Modeling https://tess.elixir-europe.org/events/advanced-statistics-statistical-modeling-6f35f6b7-7d91-47b8-8ae4-3c447f2dd0da Overview While the statistical models and tools presented in an introductory statistics course (such as linear regression) can be used to answer a wide range of questions in life sciences, many types of data can not be analyzed using these tools. 2020-08-17 09:00:00 UTC 2020-08-20 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Protein Bioinformatics: Sequence-Structure-Function - Dates to be confirmed

    18 - 20 November 2020

    Basel, Switzerland

    Elixir node event
    Protein Bioinformatics: Sequence-Structure-Function - Dates to be confirmed https://tess.elixir-europe.org/events/protein-bioinformatics-sequence-structure-function-dates-to-be-confirmed Overview Sequence-structure-function relationships of proteins are central to a comprehensive understanding of cellular biology. However, many proteins lack direct and detailed information regarding structure, function, and complex formation. 2020-11-18 09:00:00 UTC 2020-11-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First Steps with Perl in Life Sciences

    24 - 25 June 2020

    Lausanne, Switzerland

    Elixir node event
    First Steps with Perl in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-perl More information soon 2020-06-24 09:00:00 UTC 2020-06-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • neXtProt - an introduction

    24 September 2020

    Geneva, Switzerland

    Elixir node event
    neXtProt - an introduction https://tess.elixir-europe.org/events/nextprot-an-introduction More information soon 2020-09-24 09:00:00 UTC 2020-09-24 00:00:00 UTC SIB, Geneva, Switzerland SIB Geneva Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • First Steps with UNIX in Life Sciences

    23 September 2020

    Lausanne, Switzerland

    Elixir node event
    First Steps with UNIX in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-unix-in-life-sciences-a8e36e3f-7bff-40fb-bc07-755d310fe911 Overview With a constant evolution of technologies, life scientists (such as laboratory biologists) are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis. 2020-09-23 09:00:00 UTC 2020-09-23 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Introduction to high-performance computing (sciCORE cluster) - streamed

    3 June 2020

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to high-performance computing (sciCORE cluster) - streamed https://tess.elixir-europe.org/events/introduction-to-high-performance-computing-scicore-cluster-17743d87-92b4-473f-9591-384d43fe776d This course will be streamed only for the registered participants. Registered participants will receive specific information directly from the respective course’s organizers. This course is currently over-subscribed with a waiting list. 2020-06-03 09:00:00 UTC 2020-06-03 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Ligand-protein docking, and computer-aided drug design

    3 - 5 November 2020

    Lausanne, Switzerland

    Elixir node event
    Ligand-protein docking, and computer-aided drug design https://tess.elixir-europe.org/events/ligand-protein-docking-and-computer-aided-drug-design-a6576d32-6b99-4155-a68c-d273db65592a Overview This workshop aims to present basics on molecular visualization, ligand-protein docking and several computer-aided drug design tools developed at SIB. Numerous case examples are taken from different therapeutic fields. 2020-11-03 09:00:00 UTC 2020-11-05 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • NGS bioinformatics quality control and variant annotation for cancer diagnosis

    14 September 2020

    Bern, Switzerland

    Elixir node event
    NGS bioinformatics quality control and variant annotation for cancer diagnosis https://tess.elixir-europe.org/events/ngs-bioinformatics-quality-control-and-variant-annotation-for-cancer-diagnosis-46eda521-132e-4796-a920-cbbe89f76182 Overview This course is organised by SIB Swiss Institute of Bioinformatics, in collaboration with the Clinical Pathology Division of the University Hospital of Geneva (HUG). 2020-09-14 09:00:00 UTC 2020-09-14 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Enrichment Analysis - streamed

    26 June 2020

    Streamed from Lausanne, Switzerland

    Elixir node event
    Enrichment Analysis - streamed https://tess.elixir-europe.org/events/enrichment-analysis-streamed We are sorry but this course is oversubscribed, with a long waiting list. 2020-06-26 09:00:00 UTC 2020-06-26 00:00:00 UTC SIB, Streamed from Lausanne, Switzerland SIB Streamed from Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Introduction to Machine Learning - streamed

    22 - 23 July 2020

    Streamed from Greece and Mauritius, Switzerland

    Elixir node event
    Introduction to Machine Learning - streamed https://tess.elixir-europe.org/events/introduction-to-machine-learning-streamed We are sorry but this course is oversubscribed, with a long waiting list. Sign up here to be informed of the next course. 2020-07-22 09:00:00 UTC 2020-07-23 00:00:00 UTC SIB, Streamed from Greece and Mauritius, Switzerland SIB Streamed from Greece and Mauritius Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []