VectorBase Seth Redmond Imperial College, London

Slides:

Advertisements

Similar presentations

Genome Annotation: A Protein-centric Perspective.

Advertisements

Neglected Tropical Diseases and Malaria: The need for mapping.

VectorBase Frank Collins, Scott Emrich, Dan Lawson,Greg Madey BRC PI/PM Meeting Bethesda, MD April 27, 2012.

Towards an ontology of vector- borne diseases: MalIDO, the first step.

Classification of Parasites

Glossina Transcriptome Annotation Karyn Megy, VectorBase European Bioinformatics Institute, UK.

Effects of climate change on transmission of vector-borne diseases Howard S. Ginsberg, Ph.D. USGS Patuxent Wildlife Research Center University of Rhode.

Intro Medical parasitology: the study and medical implications of parasites that infect humans. Molecular parasitology: the study of the molecular biology.

Climate Change and Vector-Borne Disease Durland Fish, Ph.D. Yale School of Public Health Yale School of Forestry and Environmental Studies.

Differential insertion of transposable elements in Anopheles gambiae M & S genomes Jenica L. Abrudan, Ryan C. Kennedy, Maria F. Unger, Michael R. Olson,

Session I: Creating Institutional Structures for Community Level IPM Karl Malamud-Roam, IR-4 Project John Carroll, USDA.

Medical Diagnostics NIAID Funding Opportunities Maria Y. Giovanni, Ph.D. Assistant Director for Microbial Genomics and Advanced Technologies National Institute.

VectorBase Invertebrate Vectors of Human Pathogens.

BRC6 28 th October 2008 Collective annotation of the Ixodes scapularis genome: VectorBase, MSCs and the tick community. Daniel Lawson, VectorBase.

NIAID Bioinformatics Resource Centers Valentina Di Francesco Bioinformatics Program Director Microbial Genomics Program, DMID.

Specie: Anopheles gambiae PEST Genome size: 260 Mb Status: 3rd assembly and annotation NIAID funded.

Graduate Opportunities in Bioinformatics By Tristan Butterfield Alternative Career Presentation Senior Seminar,

ABSTRACT We have conducted an extensive computational analysis of the Culex quinquefasciatus genome to find and annotate a specific subfamily of the TEs:

Genome Annotation BCB 660 October 20, From Carson Holt.

Eastern Africa Barcode Workshop, Oct DNA Barcoding - Parasites and Vectors Dan Masiga Molecular Biology and Biotechnology Department.

Richard H. Scheuermann, Ph.D. Department of Pathology Division of Biomedical Informatics U.T. Southwestern Medical Center Standardizing Metadata Associated.

EBI is an Outstation of the European Molecular Biology Laboratory. Every genome deserves a home Dan Lawson EMBL-EBI.

Scott Emrich Assistant Professor, Computer Science and Engineering Scientific Manager, VectorBase University of Notre Dame A flexible, scalable genomics.

thing entity continuant dependent_continuant specifically_dependent_continuant realizable_entity dispositionvector_borne_diseaseOntologies &

VectorBase A Resource Centre for Invertebrate Hosts of Human Pathogens Bob MacCallum Imperial College London.

Abstract Although transposable elements (TEs) were discovered over 50 years ago, the robust discovery of them in newly sequenced genomes remains a difficult.

Kerstin Howe, Mario Caccamo, Ian Sealy The Zebrafish Genome Sequencing Project Bioinformatics resources.

Rhesus genome annotations Rob Norgren Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical Center.

EBI is an Outstation of the European Molecular Biology Laboratory. Bert Overduin Daniel Rios Stephen Fitzgerald Edinburgh, 24 & 25 February 2009 Ensembl.

Annotation of Anopheline Genomes at VectorBase Dan Lawson, VectorBase & The Anopheles Genomes Cluster Consortium EMBL-EBI.

The new VectorBase: our improved resource for invertebrate vectors Scott Emrich On behalf of VectorBase “bigger, better, faster” Or “ "consolidate, improve.

VectorBase Gene expression data in VectorBase Fotis Kafatos, George Christophides, Bob MacCallum & Seth Redmond Imperial College London (thanks also to.

DAN LAWSON BRC 2011 – ANNUAL MEETING UT SOUTHWESTERN MEDICAL CENTER DALLAS, TX SEPTEMBER 2011 Challenges and opportunities of new sequencing technologies.

MAKER Annotation Process Example of Glossina VectorBase Karyn Mégy Dan Hughes.

Web Apollo and the VectorBase user community Gloria I. Giraldo-Calderón March 31, 2015.

DAY 1c: Accessing Completed Genomes 1. UCSC Genome Bioinformatics 2. Ensembl 3. NCBI Genomic Biology.

Parasitic Helminths and Arthropod Agents and Vectors of Diseases.

VectorBase BRC The evolving VectorBase gene build: mixing automated and manual approaches when annotating vector genomes Daniel Lawson VectorBase-EBI,

Vectorbase and Galaxy Jarek Nabrzyski On behalf of VectorBase Center for Research Computing University of Notre Dame VectorBase Bioinformatics Resource.

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

2009 GMOD Meeting Dhileep Sivam & Isabelle Phan Seattle Biomedical Research Institute.

VectorBase BRC Overview Scott Emrich BRC 2011 – Annual Meeting UT Southwestern Medical Center Dallas, TX September 2011.

Annotating genomes using MAKER-P and iPlant. What Are Annotations? Annotations are descriptions of features of the genome –Structural: exons, introns,

Importing Community annotations into VectorBase. Aims Provide the VectorBase community with tools for improving genome annotation. Must have low entry.

Interactions with other BRCs Scott Emrich “all hands” meeting VectorBase.

VectorBase Kolymbari Meeting July 2011 new genomes new features and future plans Daniel Lawson (on behalf of VectorBase)

Map-based Exploration of Population Biology Data in VectorBase What is VectorBase? We are a consortium of institutions that hosts the genomes of invertebrate.

VectorBase Vectorbase probe mapping. VectorBase Automatic Annotation browser Array data CHADO Manual Annotation XML vectorbase Automatic Annotation.

Overview and History of VectorBase Frank Collins March 31, 2015.

9/10/06 GO Users Meeting 2006 Seattle, Washington The AgBase GO Annotation Tools Susan Bridges 1,3, Fiona McCarthy 2,3, Nan Wang 1,3, G. Bryce Magee 1,3,

EBI is an Outstation of the European Molecular Biology Laboratory. Gautier Koscielny VectorBase Meeting 08 Feburary 2012, EBI VectorBase Text Search Engine.

VectorBase’s Population Biology Resources and How to Submit to Them Bob MacCallum Imperial College, London, UK July 16, 2013.

Parasitic Helminths and Arthropod Agents and Vectors of Diseases.

Protozoa Trypanosomes.

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

INTRODUCTION TO ENVIRONMENTAL MEDICINE (2) By Dr. Khalid El Tohami.

Immunology Ontology Rho Meeting October 10, 2013.

Human features are those things created by man.

VectorBase genome annotation

Bioinformatics Tools for Comparative Genomics of Vectors

Infectious Disease: A New Challenge for Biomedical Informatics

James H. Diaz, MD, MPH&TM, DrPH Wilderness & Environmental Medicine

Functional Annotation of the Horse Genome

James H. Diaz, MD, MPH&TM, DrPH Wilderness & Environmental Medicine

Insect and pest control

Current status, problems and why a new approach is necessary

Genome Annotation w/ MAKER

KEY CONCEPT Arthropods and humans interact in many ways.

KEY CONCEPT Arthropods and humans interact in many ways.

Infectious Diseases images.google.com/imgres?imgurl=

Presentation transcript:

VectorBase Seth Redmond Imperial College, London

VectorBase “A Relational Bioinformatics Resource Center for Arthropod Vectors of Human pathogens” Funded by NIAID (National Institute of Allergy & Infectious Diseases - US) One of a set of BRC’s funded to support large-scale sequencing projects

VectorBase Aedes aegyptii (Yellow Fever) A.gambiae (PEST) (Malaria) A.gambiae (M)A.gambiae (S) Culex pipens (Filariasis) Pediculus humanus (Misc - body louse) Ixodes Scapularis (Lyme Disease) Lutzomyia longipalpis (Leishmaniasis) Glossina Morsitans (Sleeping sickness) Rhodnius prolixus (Chagas Disease) Phlebotomus papatasi (Leishmaniasis)

VectorBase PROBE ALIGNS COMP ANNOT MAN ANNOT EST ANNOT MAN ANNOT PROT ANNOT HOSTING & INTEGRATION

VectorBase

CEGG APOLLO DAS server DAS server DAS server DAS server DAS server DAS client

VectorBase APOLLO CEGG

VectorBase VB DAS use e! DAS client Permanent DAS servers: Rapidly changing features –e.g. manual annotation Low priority / low usage features –e.g. AnoEST clusters ‘Temporary’ servers Preliminary data –e.g. array mappings between genebuilds Collaborative use

VectorBase Permanent Servers A Gambiae –Manual annotation VectorBase manual CEGG Immunity set –Comp annotation AnoEST Clusters ReAnoCDS –Transposons A.Aegypti –Comp Annotation AedEST Clusters

VectorBase APOLLO CEGG

VectorBase APOLLO CEGG

VectorBase APOLLO CEGG DAS server DAS server DAS client DAS server

VectorBase DAS requests… Versioning –Old features / New assemblies Nested Features –Sim to GFF3, refer to parent ID to allow construction of gene models

VectorBase Imperial –Fotis Kafatos –George Christophides –Bob Maccallum EBI –Ewan Birney –Dan Lawson –Martin Hammond –Karyn Megy Harvard –William Gelbart –Susan Russo –Kathy Campbell Notre Dame –Frank Collins –Rob Bruggner –EO. Stinson –Neil Lobo IMBB –Kitsos Louis –Pantelis Topalis