Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

• How to connect Galaxy to a compute cluster?
• How can I configure job dependent resources, like cores, memory for my DRM?

Objectives of the tutorial:

• Be familiar with the basics of installing,...

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

• How does Galaxy manage users and groups?
• How can I assign Quotas to specific users/groups?

Objectives of the tutorial:

• Learn the Galaxy user/group management and assign Quotas.
• Understand...

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

• How to convert LC-MS/MS raw files?
• How to identify peptides?
• How to identify proteins?
• How to evaluate the results?

Objectives of the tutorial:

• Protein identification from LC-MS/MS raw files.

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

• How can protein N-termini be enriched for LC-MS/MS?
• How to analyze the LC-MS/MS data?

Objectives of the tutorial:

• Run an N-TAILS data analysis.

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

• How is the Galaxy code structured?
• What do the various other projects related to Galaxy do?
• What...

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

• What are Galaxy Webhooks?
• How to create them?

Objectives of the tutorial:

• Discover what Galaxy...

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

• What are Galaxy Interactive Environments (GIEs)?
• How to enable GIEs in Galaxy?
• How to develop your own...

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

• How can I make a custom plugin for Charts?

Objectives of the tutorial:

• Learn how to add custom...

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

• What is a Galaxy Interactive Tour?
• How to create a Galaxy Interactive Tour?

Objectives of the...

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

• How to identify the genetic variation with the use of exome sequencing?
• What is the pipeline of the process of finding genetic variation which caused the disease?

Objectives of the...

Resources related to configuration and maintenance of Galaxy servers

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

• Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that
• How to extract usage information,...

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

• Why Docker? What is it?
• How to use Docker?
• How to integrate Galaxy in Docker to facilitate its deployment?

Objectives of the tutorial:

• Docker basics
• Galaxy Docker image (usage)
• Galaxy...

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

• Which coding exon has the...

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

• How to use Galaxy?
• How to get...

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

• What are MS1 features?
• How to quantify based on MS1 features?
• How to map MS1 features to MS2 identifications?
• How to evaluate and optimize the results?

Objectives of the tutorial:

• MS1 feature...

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

• How to convert LC-MS/MS raw files?
• How to identify peptides?
• How to identify proteins?
• How to evaluate the results?

Objectives of the tutorial:

• Protein identification from LC-MS/MS raw files.

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

• How to predict cellular protein localization based upon GO-terms?
• How to combine multiple localization predictions?

Objectives of the tutorial:

• Predict proteins in the cellular secretome by using...

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

• What are benefits and drawbacks of different quantitation methods?
• How to choose which quantitation method bests suits my need?

Objectives of the tutorial:

• Choose your quantitation method.

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

• How to download protein FASTA databases of a certain organism?
• How to download a contaminant database?
• How to create a decoy database?
• How to combine databases?

Objectives of the tutorial:

• Creation of a...

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...

An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday.
Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...