Pfam Pfam & DAS Rob Finn 26 th Feb 2007. Pfam Acknowledgements John Tate Roger Pettett Andreas Prlic Andy Jenkinson But takes data from community…..!

Slides:

Advertisements

Similar presentations

Protein Annotation Ontology The BioSapiens Virtual Institute for Genome Annotations Janet Thornton & Gabby Reeves AFP/BioSapiens Vienna: July 07.

Advertisements

DEPARTMENT OF INFORMATION STUDIES Andy Dawson LIS1510 Library and Archives Automation Issues Further features of XHTML – Stylesheets and CSS Andy Dawson.

EBI is an Outstation of the European Molecular Biology Laboratory. DAS implementations Bernat Gel 01/03/11.

Andy Jenkinson, EBI The DAS Protocol. Summary of Topics Technical overview Principles of communication Pros and cons DAS capabilities.

Andy Jenkinson, EBI An Introduction to DAS. Summary of Topics What is Data Integration? Problems in Data Integration An architectural overview of DAS.

Andy Jenkinson, EBI An Introduction to DAS. Summary of Topics What is Data Integration? Problems in Data Integration An architectural overview of DAS.

A component- and message-based architectural style for GUI software

PHP for Server-Side Preprocessing Chapter 08. Overview and Objectives Present a brief history of the PHP language Discuss how PHP fits into the overall.

4.01 How Web Pages Work.

Rafael C Jimenez DAS DAS Workshop 2012 February 27-29, 2012 Using DAS software, an introduction to some DAS implementations.

Peter Rice and Mahmut Uludag EMBOSS as an Efficient DAS Annotation Source Peter Rice, EBI Mahmut Uludag, EBI 10th March.

W alkie Doggie is a web application that allows dog owners to help each other with their dog walks. It’s main feature is the walkies, which are the user’s.

Structural Biology and Biocomputing Programme 1 Osvaldo Graña, CNIO Distributed Annotation System (DAS) part I Osvaldo Graña VIII.

Design of Web-based Systems IS Development: lecture 10.

The Internet Useful Definitions and Concepts About the Internet.

Does Ajax suck? CS575 Spring 2007 Chanwit Suebsureekul.

Topics in this presentation: The Web and how it works Difference between Web pages and web sites Web browsers and Web servers HTML purpose and structure.

A Customisable Question and Answer Database Kate Lindsay.

Presented By: Ayelet Birnbaum Yael Kazaz Supervisor: Viktor Kulikov 07/05/12.

A content management system (CMS) is a computer program that allows publishing, editing and modifying content on a web site as well as maintenance from.

New logging and notification system for the Offline DropBox Martynas Mitrulevičius Thursday, 26 April 2012 AlCaDB/PdmV meeting Vilnius University, Lithuania.

Moving forward our shared data agenda: a view from the publishing industry ICSTI, March 2012.

Update on the DAS Registry DAS Workshop 2011 Jonathan Warren.

Viewing & Getting GO COST Functional Modeling Workshop April, Helsinki.

Generating Intelligent Links to Web Pages by Mining Access Patterns of Individuals and the Community Benjamin Lambert Omid Fatemieh CS598CXZ Spring 2005.

The National Center for Atmospheric Research is operated by the University Corporation for Atmospheric Research under sponsorship of the National Science.

DAS Game DAS game Distributed Annotation System A game to settle down the concept of DAS Game cards available in:

Web Mashups -Nirav Shah.

Multimodal Alignment of Scholarly Documents and Their Presentations Bamdad Bahrani JCDL 2013 Submission Feb 2013.

Fission Yeast Computing Workshop -1- Searching, querying, browsing downloading and analysing data using PomBase Basic PomBase Features Gene Page Overview.

Universiti Utara Malaysia Chapter 3 Introduction to ASP.NET 3.5.

The Pfam and MEROPS databases EMBO course 2004 Robert Finn

LOGO 2 nd Project Design for Library Programs Supervised By Dr: Mohammed Mikii.

Understanding AJAX Hype, Hope, Hurt and Help for the Web MJTS May 4th, 2006 _________________________ Terence Conklin, Conklin Systems

Adding GO for Large Datasets COST Functional Modeling Workshop April, Helsinki.

DAS for Molecular Interactions Hagen Blankenburg.

Joe Hummel, PhD Dept of Mathematics and Computer Science Lake Forest College

DAP4 James Gallagher & Ethan Davis OPeNDAP and Unidata.

Introduction to DAS / State of the Union Tim Hubbard DAS developer workshop 10th March 2009 Wellcome Trust Genome Campus.

Searching the web Enormous amount of information –In 1994, 100 thousand pages indexed –In 1997, 100 million pages indexed –In June, 2000, 500 million pages.

MsSEM.comHelen M. Overland MsSEM.com The Canonical URL Tag How to Use the Canonical Tag to Avoid Duplicate Content Filters in Google, Yahoo & Live.

Pfam, DAS and the future Rob Finn DAS Workshop 2009.

Alastair Kerr, Ph.D. WTCCB Bioinformatics Core An introduction to DNA and Protein Sequence Databases.

1 Yield Analysis and Increasing Engineering Efficiency Spotfire Users Conference 10/15/2003 William Pressnall, Scott Lacey.

World Wide Web “WWW”, "Web" or "W3". World Wide Web “WWW”, "Web" or "W3"

Orthology & Paralogy Alignment & Assembly Alastair Kerr Ph.D. [many slides borrowed from various sources]

DAS Current Situation and Future Developments Jonathan Warren DAS coordinator for the Sanger Institute

EBI is an Outstation of the European Molecular Biology Laboratory. easyDAS Automatic DAS server creation Bernat Gel Universitat Politècnicade Catalunya.

Orthology & Paralogy Alignment & Assembly Alastair Kerr Ph.D. WTCCB Bioinformatics Core [many slides borrowed from various sources]

WILLY’S STRAWBERRY FACTORY Website Proposal. WEBSITE CONTENT Photo galleries of the factory Directions via Google Maps embedded on the website Pricing.

The Protein Identifier Cross-Reference (PICR) service.

DAS Advance Search and its prototype implementation in MyDas Gustavo Adolfo Salazar Orejuela Supervised by: Nicola Mulder Henning Hermjakob DAS workshop.

Dasty2 DAS workshop th March Rafael Jimenez.

Jalview Visualising DAS annotation on Multiple Sequence Alignments 26 th February 2007 Andrew Waterhouse

8 th Semester, Batch 2009 Department Of Computer Science SSUET.

(ITI310) By Eng. BASSEM ALSAID SESSIONS 10: Internet Information Services (IIS)

Ensembl DAS and Ensembl The 7 year itch!. Ensembl DAS and Ensembl The 7 year itch! A brief history DAS ist gut Issues Some proposals.

Google Code Libraries Dima Ionut Daniel. Contents What is Google Code? LDAPBeans Object-ldap-mapping Ldap-ODM Bug4j jOOR Rapa jongo Conclusion Bibliography.

Enlargement Simple scale factors. Find the scale factor and the missing length ?

Human features are those things created by man.

Web Server Architecture/Hosting Capstone Project2 Name-ASFAQUE KHAN Regno

Web Mashups -Nirav Shah.

Web page a hypertext document connected to the World Wide Web.

DWR: Direct Web Remoting

Large Scale Annotation of Genomic Datasets with Genephony

World Wide Web “WWW”, "Web" or "W3". World Wide Web “WWW”, "Web" or "W3"

World Wide Web “WWW”, "Web" or "W3". World Wide Web “WWW”, "Web" or "W3"

DD Sir-Infomatics Web Development Part-1.

OpenURL: Pointing a Loaded Resolver

Presentation transcript:

Pfam Pfam & DAS Rob Finn 26 th Feb 2007

Pfam Acknowledgements John Tate Roger Pettett Andreas Prlic Andy Jenkinson But takes data from community…..!

Pfam New Pfam Website!

Pfam New Pfam Website! DAS Enabled

Pfam What do we provide? Pfam Domains Active Sites Other sequence Features Alignments Alignment features

Pfam Pfam Alignment Client Motivation –Simple alignment client Not trying to reinvent Jalview –Markup alignment –Pfam alignments vary in size Paging

Pfam Pfam Alignment Client Example - combines alignment and features requests

Pfam Pfam Features Client Motivation –Include Other annotations Identify where we are missing domains –Reduce data duplication –Allow tailored views –Enrich single protein data in Pfam

Pfam Pfam Features Client

Pfam Other Datasets

Pfam What Code Base? Pfam is Perl orientated –Server ProServer (CPAN) –Client Bio::Das::Lite (CPAN) Bio::Pfam::Drawing –Break out?

Pfam What Can’t I Do (with Das)? Asynchronous requests –Return pfam_scan results via DAS Mapping experimental datasets to public datasets Serve Pfam Textual Annotation –SOAP implementation

Pfam What is Hard to Do? Large scale analyses Filter out rubbish! –But what is one man’s rubbish…. Requirement for stylesheet? Standard Graphics library?

Pfam What Worries Me? Data deluge –Make Views….? Other people serve Pfam data –Confusion…..? –Redundancy People always want more from clients

Pfam Thank you!