2 events found
Using the Human Protein Atlas – Tips and Tricks
3 December 2016
San Francisco, United States of AmericaUsing the Human Protein Atlas – Tips and Tricks http://www.ascb.org/2016meeting/subgroupl/ https://tess.elixir-europe.org/events/using-the-human-protein-atlas-tips-and-tricks Organizer: Tove Alm, KTH Royal Institute of Technology This practical workshop will give you knowledge on why and how to use the Human Protein Atlas database (www.proteinatlas.org). The Human Protein Atlas portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in normal human tissues, cancer tissues, and different human cell lines. Antibody-based methods have been used together with transcriptomic analysis to explore the human proteome. The data are publicly available and include application-specific validations for each antibody. During the workshop different areas of the Protein Atlas will be explored, with a focus on the new Cell Atlas launching Dec. 4, 2016. Practical questions will be handed out that are solved by hands-on use of the Human Protein Atlas. Presentations: 1:30-1:35 pm – Welcome. Tove Alm, KTH Royal Institute of Technology 1:35-1:55 pm – Introduction to the Human Protein Atlas. Mathias Uhlén, KTH Royal Institute of Technology 1:55-2:15 pm – Spatial localization of proteins in the Tissue Atlas. Cecilia Lindskog, Uppsala University 2:15-2:35 pm – All about the Pathology Atlas. Fredrik Pontén, Uppsala University 2:35-2:45 pm – Break 2:45-3:05 pm – High-resolution: The Cell Atlas. Emma Lundberg, KTH Royal Institute of Technology 3:05-3:25 pm – Antibody validation for bioimaging. Lars Björk, KTH Royal Institute of Technology 3:25-3:45 pm – Working with the downloadable Human Protein Atlas data. Kalle von Feilitzen, KTH Royal Institute of Technology 3:45-3:55 pm – Concluding remarks and future prespective. Mathias Uhlén, KTH Royal Institute of Technology 3:55-4:10 pm – Break 4:10-5:30 pm – Practical session with General Questions and Answers 2016-12-03 13:30:00 UTC 2016-12-03 17:30:00 UTC ASCB 2016 Moscone Center, San Francisco, United States of America Moscone Center San Francisco San Francisco County United States of America Protein databases Protein expression  Tove Alm, KTH Royal Institute of Technology email@example.com  Life Science Researchers meetings_and_conferencesworkshops_and_courses  protein family databasesImaging
Multiple Sequence Alignment with Jalview and Protein Structure and Function Modelling
14 - 15 May 2018
Liverpool, United KingdomMultiple Sequence Alignment with Jalview and Protein Structure and Function Modelling http://www.jalview.org/training/training-courses/Multiple-Sequence-Alignment-with-Jalview-and-Protein-Structure-and https://tess.elixir-europe.org/events/multiple-sequence-alignment-with-jalview-and-protein-structure-and-function Date: Monday 14th to Tuesday 15th May 2018 Time: 9.00 to 17.00 Location: MSTC, Sherrington Building, University of Liverpool, L69 3BX Overview This two day hands-on training course is aimed at students and researchers who want to gain practical understanding of the tools and approaches for protein sequence, structure and function prediction and analysis. In day 1, participants will be introduced to Jalview - a free desktop application for the visualisation and comparative analysis of protein, DNA and RNA sequences. Jalview can integrate data from Ensembl, Uniprot, PDBe, Rfam and Pfam, and can access a range of tools for multiple sequence alignment, conservation analysis and secondary structure and disorder prediction, including the widely used JPred4. On the second day, participants will learn to use Jalview’s 3D structure visualisation capabilities in conjunction with UCSF Chimera, and take a whistle-stop tour of the methodologies and tools for prediction and analysis of Protein 3D structure and function. Participants are encouraged to bring their own protein analysis problems and time will be reserved at the end of day 2 for discussion. Register using the link on the Jalview website: http://www.jalview.org/training/training-courses/Multiple-Sequence-Alignment-with-Jalview-and-Protein-Structure-and Day 1: Multiple Sequence Alignment and Analysis with Jalview Workshop trainers: Dr Jim Procter and Dr Suzanne Duce 9 9.15 Introduction to the Workshop 9.15 10.30 Session 1.Loading sequences, structures and alignments with Jalview Coffee break 11 12.30 Session 2. Multiple alignment Creation and Alignment Reliability Lunch 1.30 3pm Session 3. Phylogenetic trees and subfamily analysis of Proteins and CDS Coffee break 3.30 5pm Session 4. Protein secondary structure and disorder prediction, and working with annotation Day 2: Protein Structure Analysis and Modelling Workshop trainers: Dr Jim Procter and Dr Dan Rigden 9 9.15 Introduction to Workshop Day 2 9.15 9.30 Introduction to Protein 3D Structure 9.30 10 Viewing and Comparing 3D structures with Jalview and UCSF Chimera 10 10.30 Mapping sequence conservation to Biological Assemblies with Jalview Coffee Break 11 12.30 Functional analysis of Protein Structures Lunch 1.30 2.30 Homology modelling and model quality evaluation 2.30 3.15 Ab initio models and searching for fold matches 3.15 3.30 Wrap up: Function Analysis and 3D models Coffee Break 4pm 5pm Analyse your own protein sequences and structures. 2018-05-14 09:00:00 UTC 2018-05-15 17:00:00 UTC Dr Jim Procter and Dr Dan Rigden MSTC, Sherrington Building, University of Liverpool, Liverpool, United Kingdom MSTC, Sherrington Building, University of Liverpool Liverpool Merseyside United Kingdom L69 3BX University of Liverpool Dr Jim Procter and Dr Suzanne Duce, School of Life Sciences, University of Dundee, Dundee University of Dundee PhD studentspostdoctoral researchersprinciple investigatorsLife Science Researchersbioinformaticians 45 workshops_and_courses registration_of_interest Jalviewmultiple sequence alignmentMSAprotein sequence protein structure protein predictionHomology modellingAb initio modelsChimerasubfamily analysisPhylogenetic treesProtein secondary structureUniversity of DundeeUniversity of Liverpool
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