Recursos en línea y análisis de datos biológicos
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Visión general
Esta serie de seminarios web proporciona una descripción general de los recursos de datos disponibles públicamente, con énfasis en los proporcionados por el Instituto Europeo de Bioinformática
La serie forma parte del currículo del Máster en Biología Computacional en la Universidad de los Andes. Nos gustaría explorar la posibilidad de que otras universidades participen en este módulo en el futuro. ¿Por qué no unirse a nosotros para experimentar el módulo y obtener más información?
Tenga en cuenta que estos seminarios web normalmente no se grabarán porque forman parte de una clase de bioinformática en vivo. Deberás registrarte con anticipación para unirte.
Audiencia
Esta serie es adecuada para estudiantes graduados y superiores en ciencias de la vida molecular, o incluso para cualquier persona que trabaje en ciencias biomoleculares que deseen familiarizarse con la riqueza de datos biológicos disponibles en el dominio público. También agradecemos la participación de los directores y profesores de los cursos, para que puedan evaluar si el contenido puede ser útil para sus propios cursos.
Resultados
- Evaluar el papel de la bioinformática en la investigación de ciencias de la vida molecular.
- Reconocer los principales tipos de recursos de datos públicos para la investigación biomolecular.
- Seleccione los recursos apropiados para explorar conjuntos de datos de interés para su investigación
- Describir las características clave de las bases de datos primarias y secundarias.
- Listar estrategias para describir datos consistentemente
- Identifique algunos de los diferentes tipos de análisis de datos que se pueden aplicar para resolver problemas biológicos
Programa
Serie de seminarios web 2019
| Semana | jueves fecha | Hora de clase (UTC) | Título | Estudio previo al seminario web | Entrenadora | Página web y registro |
| 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 | |
| 5 | 5th September | 14:30-15:50 | Ensembl 1 webinar | - | Emily Perry | |
| 6 | 12th September | 14:30-15:50 | Ensembl 2 webinar | - | Emily Perry | |
| 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 | |
| 8 | 26th September | 14:30-15:50 | Introduction to Programmatic Access | Take a rest... | Alejandro Reyes | |
| 9 | 3rd October | - | - | - | - | - |
| 10 | 10th October | 14:30-15:50 | Protein sequence to function with UniProt | UniProt: Exploring protein sequence and functional information | Hema Bye-A-Jee | |
| 11 | 17th October | 14:30-15:50 | Functional analysis of proteins with InterPro | InterPro: functional and structural analysis of proteins | Lorna Richardson | |
| 12 | 24th October | 14:30-15:50 | Understanding protein structures with PDBe | PDBe - searching for biological macromolecular structures | David Armstrong / Deepti Gupta | |
| 13 | 31st October | 14:30-15:50 | Exploring molecular interactions with IntAct | IntAct: molecular interactions at EMBL-EBI | To be confirmed | |
| 14 | 7th November | 14:30-15:50 | Biological pathways with Reactome | Reactome: exploring biological pathways | Thawfeek Varusai | |
| 15 | 14th November | 14:30-15:50 | Programmatic Access 2 |
Serie de seminarios web 2018
Jueves 15 de noviembre
09: 30–10: 50 hora de Colombia / 15: 30–16: 50 hora de verano británica / 14: 30–15: 50 UTC (verifica tu zona horaria)
Acceso programático 2
Con Leyla García, Senior Software Engineer - Martin team: Protein Function development [sobre Leyla]
Tome un RESTO de las búsquedas manuales y únase a nosotros en este seminario web para obtener más información sobre el acceso programático para los recursos de EBI con un énfasis especial en los servicios REST de UniProt.
Estudio Pre-Webinar:
https://www.ebi.ac.uk/training/online/course/embl-ebi-programmatically-take-rest-manual-searches
Puede hacer preguntas y participar en discusiones con otros participantes usando Slack
Webinars anteriores en esta serie
Jueves 08 noviembre
09: 30–10: 50 hora de Colombia / 15: 30–16: 50 hora de verano británica / 14: 30–15: 50 UTC
Vías biológicas con Reactome.
Con Thawfeek Varusai, Scientific Database Curator - Hermjakob team [sobre Thawfeek]
En este seminario web, aprenderá cómo usar Reactome de manera efectiva para buscar y acceder a vías biológicas y reacciones celulares. También podrá analizar datos experimentales utilizando las diversas herramientas disponibles en el recurso.
Pre-webinar Study:
- Reactome: Exploring biological pathways
Estimated study time: 2.5 Hours
Thursday 01 November
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
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
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
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
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
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
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
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
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
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