Online Resources and Biological Data Analysis
Join us for our webinar series!
Overview
This webinar series provides an overview of publicly available data resources, with an emphasis on those provided by the European Bioinformatics Institute.
The series forms part of the curriculum for the Master in Computational Biology at the University of the Andes, with CABANA partner Prof. Alejandro Reyes Muñoz as module leader. We would like to explore the possibility of other universities participating in this module in the future. Why not join us to experience the module and find out more?
Please note: these webinars will not typically be recorded because they form part of a live bioinformatics class. You will need to register in advance to join and a maximum of 20 online participants can attend, on a first come first serve basis.
Audience
This series is suitable for graduate students and above in the molecular life sciences, or indeed anyone working in the biomolecular sciences wishing to familiarise themselves with the wealth of biological data available in the public domain. We also warmly welcome the participation of course directors and lecturers, so that they can gauge whether the content might be useful for their own courses.
Outcomes
- Assess the role of bioinformatics in molecular life-science research
- Recognise the major types of public data resources for biomolecular research
- Select appropriate resources to explore data sets of interest to your research
- Describe the key features of primary and secondary databases
- List strategies for describing data consistently
- Identify some of the different types of data analysis that can be applied to solving biological problems
Programme
Webinar series 2019
| Week | Thursday date | Class time (UTC) | Webinar title | Pre-webinar study | Trainer | Webpage and registration info |
| 1 | 8th August | 14:30-15:50 | Passport to a world of biodata | - | Cath Brooksbank and Alejandro Reyes | https://www.ebi.ac.uk/training/events/2019/cabana-webinar-passport-world-biodata |
| 2 | 15th August | 14:30-15:50 | Introduction to ontologies |
http://drjamesmalone.blogspot.com/2018/03/hackers-guide-to-understanding... http://drjamesmalone.blogspot.com/2012/06/common-ontology-questions-1-wh... http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.10... |
Olamidipupo Ajigboye | Registration link |
| 3 | 22nd August | 14:30-15:50 | From papers to data with EuropePMC | Europe PMC quick tour | Maria Levchenko / Dayane Rodrigues Araujo | |
| 4 | 29th August | 14:30-15:50 | Introduction to the European Variation Archive | - | Baron Koylass | Registration link |
| 5 | 5th September | 14:30-15:50 | Ensembl 1 webinar | - | Emily Perry | Registration link |
| 6 | 12th September | 14:30-15:50 | Ensembl 2 webinar | - | Emily Perry | Registration link |
| 7 | 19th September | 14:30-15:50 | Exploring functional genomics with Expression Atlas | Functional genomics I-II; Expression Atlas Quick Tour | Nancy George / Silvie Fexova | Registration link |
| 8 | 26th September | No webinar | - | - | - | |
| 9 | 3rd October | No webinar | - | - | - | |
| 10 | 10th October | 14:30-15:50 | Protein sequence to function with UniProt | UniProt: Exploring protein sequence and functional information | Hema Bye-A-Jee | Registration link |
| 11 | 17th October | 14:30-15:50 | Functional analysis of proteins with InterPro | InterPro: functional and structural analysis of proteins | Lorna Richardson | Registration link |
| 12 | 24th October | 14:30-15:50 | Understanding protein structures with PDBe | PDBe - searching for biological macromolecular structures | David Armstrong / Deepti Gupta | Registration link |
| 13 | 31st October | 14:30-15:50 | Exploring molecular interactions with IntAct | IntAct: molecular interactions at EMBL-EBI | To be confirmed | Registration link |
| 14 | 7th November | 14:30-15:50 | Biological pathways with Reactome | Reactome: exploring biological pathways | Thawfeek Varusai | Registration link |
| 15 | 14th November | 14:30-15:50 | Introduction to Programmatic Access | Take a rest... | Alejandro Reyes | |
| 16 | 21st November | 14:30-15:50 | Programmatic access 2 | Andrew Nightingale |
Webinar series 2018
Thursday 15 November 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Programmatic Access 2
With Leyla García, Senior Software Engineer - Martin team: Protein Function development [about Leyla]
Take a REST from manual searches and join us in this webinar to learn more on programmatic access for EBI resources with a special emphasis on UniProt REST services.
Pre-webinar Study:
https://www.ebi.ac.uk/training/online/course/embl-ebi-programmatically-take-rest-manual-searches
You can ask questions and join in discussions with other participants using Slack
Thursday 08 November 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Biological pathways with Reactome
With Thawfeek Varusai, Scientific Database Curator - Hermjakob team [about Thawfeek]
In this webinar, you will learn how to effectively use Reactome to search and access biological pathways and cellular reactions. You will also be able to analyze experimental data using the various tools available in the resource.
Pre-webinar Study:
- Reactome: Exploring biological pathways
Estimated study time: 2.5 Hours
Thursday 01 November 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Functional analysis of proteins with InterPro
With Lorna Richardson, Protein Family Curator - Finn team: Sequence families [about Lorna]
Lorna will give an overview of the information available in InterPro, and how InterPro data is used in large-scale analysis of proteins.
Pre-webinar Study:
- Protein classification: An introduction to EMBL-EBI resources
- InterPro: Functional and structural analysis of protein sequences
Estimated study time: 3 Hours
Thursday 25 October 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Understanding protein structures with PDBe
With David Armstrong, Scientific Database Curator - Velankar team: PDBe [about David]
Thursday 18 October 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Exploring molecular interactions with IntAct
With Birgit Meldal, Scientific Database Curator (Molecular Interaction & Complexes) - Molecular Interactions [about Birgit]
Thursday 11 October 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Protein sequence to function with UniProt
With Leyla García, Senior Software Engineer - Martin team: Protein Function development [about Leyla]
Registrants have the option to vote for the specific aspect of UniProt that is most relevant or of most interest to them. Options are
- A practical walkthrough of the UniProt website for enzyme data
- Exploring protein interactions with UniProt
- Exploring models for human disease with UniProt
Registrants are first asked to complete the pre-webinar study before voting. Voting will close on 9th October. Complete the poll.
Pre-Webinar Study:
- UniProt: Exploring protein sequence and functional information
Estimated study time: 2 Hours
Thursday 27 September 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Introduction to the European Variation Archive
With Baron Koylass, Helpdesk Bioinformatician, EGA, EVA and ENA [about Baron]
Baron will provide a showcase on how to access, submit and use data from all species and variant types using the European Variation Archive.
Thursday 20 September 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Exploring functional genomics with Expression Atlas
With Laura Huerta Martinez, Senior Scientific Curator, Gene Expression [about Laura]
Laura will describe how to access and interpret gene expression analysis results with Expression Atlas. She will also explain downstream analysis results such as gene co-expression, transcript quantification and enrichment analysis.
Pre-webinar study
-
Functional Genomics (I): Introduction and designing experiments
-
Functional Genomics (II): Common technologies and data analysis methods
- Expression Atlas Quick Tour
Estimated study time: 3-4 h
Tuesday 4 September to Thursday 13 September 2018
09:00–10:50 Colombia time / 15:00–16:50 British Summer Time / 14:00–15:50 UTC (check your time zone)
Please note the earlier start time for these four webinars
Browsing genomes with Ensembl
Emily Perry, Ensembl Outreach Project Leader, EMBL-EBI [about Emily]
Astrid Gall, Ensembl Outreach Officer [about Astrid]
Erin Haskell, Ensembl Outreach Officer [about Erin]
Tuesday 4 Sep, 15:00 BST
- Introduction to Ensembl
- Ensembl region
- Ensembl genes
- Questions
- Exercises as homework
Thursday 6 September, 15:00 BST
- Variation data in Ensembl
- Comparing genes and genomes
- Questions
- Exercises as homework
Tuesday 11 September, 15:00 BST
- Finding features that regulate genes
- Data export with BioMart
- Questions
- Exercises as homework
Thursday 13 September, 15:00 BST
- Custom data
- The Ensembl Rest API
- Questions
- Exercises as homework
Pre-webinar study
There is no pre-webinar study for this series; exercises will be provided at each webinar. If you would like to familiarise yourself with Ensembl before the webinar, take a look at...
Estimated study time: 3 h
Thursday 23 August 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
From papers to data with EuropePMC
Maria Levchenko, EuropePMC Community Manager, EMBL-EBI [about Maria]
Maria will give an introduction to literature and data searches in EuropePMC, EMBL-EBI's gateway to the life science literature.
Pre-webinar study
- EuropePMC quick tour, by Michael Parkin
- EuropePMC: get the most from literature searches, by Michael Parkin
- EuropePMC author services video
- Pre-webinar exercises
Estimated study time: 2–3 h
Thursday 16 August 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
An Introduction to Ontologies
Dani Welter, Ontologist, Human Cell Atlas, EMBL-EBI [About Dani]
Dani will explain what ontologies are and how they are used to improve searching and database interoperability.
Pre-webinar study
- The hacker's guide to understanding bio-ontologies by James Malone
- Common ontology questions by James Malone
- The ontogenesis knowledge blog by Robert Stevens
- Ten simple rules for selecting a bio-ontology by James Malone et al.
Estimated study time: 2–3 h
Thursday 9 August 2018
09:30–10:50 Colombia time / 15:30–16:50 British Summer Time / 14:30–15:50 UTC (check your time zone)
Passport to a world of biodata
Cath Brooksbank, Head of Training, EMBL-EBI [about Cath]
Cath will provide an introduction to public data resources, with an emphasis on those provided by EMBL-EBI. She will summarise how data are collected and shared by the research community, why open data sharing is important, and touch on some of the different types of experiments that can be performed on biological data.
Pre-webinar study
- Create an account in our eLearning resource, Train online
- Complete Bioinformatics for the Terrified
- Complete the 10th Anniversary Treasure Hunt
Estimated study time: 2–3 h