Description
The Microarray team at the EBI attempts to address the problems of storing, managing and analyzing microarray data. ArrayExpress is a public, online repository for microarray data that conforms to the Microarray Minimum Information for a Microarray Experiment (MIAME) standards. ArrayExpress stores both normalized and well-annotated raw data from almost 16,000 hybridization studies in 35 species. Data can be submitted online and password protection to prepublication data is provided for authors and reviewers. This course will examine how to query comparative data within ArrayExpress, deposit data, and give yourself and other microarray community members’ access to your data. ExpressionProfiler, a tool written to conduct online microarray data analysis, will also be introduced.

Audience
No prior experience is required.

Format
The course consists of a 2-hour lecture OR a 4-hour hands-on workshop which duplicates the content of the lecture (see below). Lecture attendees may bring their wireless-access enabled computer laptops and follow the lecturer, as conditions permit.

• Lecture
  Registration for the lecture is unrestricted and open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. An open consultation period with EBI instructors for lecture participants will be available beginning at 3:30 PM Friday, May 20 immediately following the last EBI lecture for the week.
  
• Hands-on Workshop
  The workshop duplicates the content of the lecture, but differs in that it provides hands-on practice of the lecture demonstration examples. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor availability! Register early. Registration will be "first come - first serve." A waiting list will be maintained if necessary.

Registration
Registration is required for either the ArrayExpress lecture or workshop.

Instructors
Misha Kapushesky

Times
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Description
An overview of the sequence analysis and microarray analysis resources at Purdue, including those available at the Genomics facility, ITaP, Statistics and the Inquiry “BioTeam” cluster in Agronomy. Audience comments on how to improve bioinformatics analysis resources at Purdue will be encouraged.

Audience
No prior experience is required. Anyone with an interest in using and/or discussing in an open forum how to enhance and/or improve bioinformatic services at Purdue is encouraged to attend.

Format
The course consists of a 1 hour lecture followed by a 30 minute open consultation period.

Registration
None.

Instructors
Richard Westerman

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Description: This advanced BLAST hands-on workshop will cover the BLAST algorithm, comparing its function to other similarity search algorithms such as Needleman-Wunsch, Smith-Waterman and FASTA. The underlying statistical basis for BLAST and its relevance to search results will be covered. Advanced techniques in using similarity matrices, their derivation and use, will be presented. Specifically covered will be Position Specific Scoring Matrices (PSSM) for use in Position-Specific Iterative (PSI)-BLAST protein family searches and Pattern Hit Initiated (PHI)-BLAST protein motif searches. The use of filters as tools for BLAST searching will be illustrated and practiced, along with other “advanced commands” that can be used to enhance BLAST results.

Audience: Participants must exhibit proficiency with BLAST, the interpretation of BLAST search results, and be conceptually familiar with some of the additional topics covered (e.g., FASTA, PSI- or PHI- BLAST and/or PSSM). Registrants are expected to be familiar with the steps and processes involved in sequence similarity searching. If you are not, register for the NCBI Field Guide, the NCBI BLAST QuickStart and/or EBI’s SRS lectures/workshops.

Format: The course consists of a 4-hour hands-on workshop only. The workshop is limited to 20 participants or less to maximize interactions between instructor and student. Register early! A waiting list will be maintained with one additional session added, if necessary, sometime during Bioinformatics Week.

Registration: Registration is required for BLAST—Beyond Point and Click.

Instructor
David Osterbur

Times
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Description
The European Bioinformatics Institute (EBI) is the European equivalent to NCBI in the United States. Located on the Wellcome Trust Genome Campus in Hinxton, near Cambridge, UK, it is a legal entity with EMBL, the European Molecular Biology Laboratory, headquartered in Heidelberg, Germany, and grew out of their pioneering work to provide biological databases to the research community. In the 11 short years it has been at Hinxton, EBI has diversified to provide both bioinformatic database and bioinformatic software in all molecular domains which can overlap, complement, be alternatively indexed and curated, relative to NCBI.

This course, a general overview to the history, people and database collections of EBI, will introduce its collection of databases (~150 collated from world-wide resources and ~50 created “in-house” at EBI), software resources, and both single and cross-database search interfaces (i.e., SRS). The lecture will introduce EBI databases such as EMBL-bank (DNA and RNA sequences,) Ensembl (genomes), ArrayExpress (microarray based gene expression data), UniProt (protein sequences), MSD (macromolecular structures), ASD (alternative transcripts), and CHebi (small chemical molecules). New database and software resources, such as as IntAct (protein-protein interactions) and Reactome (pathway data), and topical resources such as genomes, will also be covered.

Audience
No prior experience is required. Aimed for both novice and experienced EBI users, the EBI Overview is designed for anyone who works with biological sequence data including principal investigators, professional staff, postdoctoral fellows, and graduate students.

Format
The course consists of a 2-hour lecture open to all principal investigators, professional staff, postdoctoral fellows, and graduate students.

Registration
Registration is required for the lecture.

Instructors
Lisa Mullan

Times
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Description
Ensembl is a joint project between EBI and the Sanger Institute which represents a stable automatic annotation of large genomes and the relationships among them. It is rapidly growing, doubling in the number of genomes provided within the last twelve months. Currently it contains Caenorhabditis, chicken, chimpanzee, cow, dog, fruitfly, Fugu, honeybee, human, mosquito, mouse, opossum, rat, Tetraodon, Xenopus and zebrafish. Ensembl has a unique gene analysis pipeline with each piece of genomic information predicted and then corroborated with biological evidence prior to display. For comparison, Ensembl also imports the data from other model organisms. Cross genome searching for ESTs, mRNAs, SNPs, proteins, diseases and more is available. This course, both lecture and workshop, is designed to present different data types available in the browser as a series of “Views”, how to compare and contrast various information from several sources and how to get the most out of the Ensembl database with the unique data-mining tool, EnsMart: A “query builder” interface which allows users to specify genomic regions and refine results. EnsMart can generate a number of different types of output, including sequence and tabulated list data.

Audience
No prior experience is required. Basic familiarity with the steps and processes involved in BLAST sequence searching, either through registration for the NCBI BLAST QuickStart demonstration-style lecture offered on Monday, May 16 or from prior experience is helpful, but not necessary.

Format
The course consists of a 2-hour lecture OR a 4-hour hands-on workshop which duplicates the content of the lecture (see below). Lecture attendees may bring their wireless-access enabled computer laptops and follow the lecturer, as conditions permit.

• Lecture
  Registration for the lecture is unrestricted and open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. An open consultation period with EBI instructors for lecture participants will be available Friday, May 20 immediately following the lecture.
  
• Hands-on Workshop
  The workshop duplicates the content of the lecture, but differs in that it provides hands-on practice of the lecture demonstration examples. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor availability! Register early. Registration will be "first come - first serve." A waiting list will be maintained if necessary.

Registration
Registration is required for either the Ensembl lecture or workshop.

Instructors
Xose Fernandez

Times
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Description
This course, a general overview of the NCBI resources, is designed to provide instruction on the effective use of NCBI’s databases, search service, the BLAST similarity search engine, genome data and related resources. Databases covered will include, but are not limited to, GenBank, RefSeq, UniGene, variation data (SNPs) and NCBI Structures. Topics will include NCBI’s genomic resources, the NCBI assembly and annotation process, the updated map viewer genome displays, the new curated conserved domains and the structural protein viewer Cn3D 4.1. Developing effective search strategies will also be covered, including database searching with Entrez and similarity searching at NCBI with the various versions of BLAST.

Audience
Aimed for both novice and experienced NCBI users, the Field Guide is continuously updated to match the changing resources at NCBI. The course has been substantially updated for 2005. It is designed for anyone who works with biological sequence data including principal investigators, professional staff, postdoctoral fellows, and graduate students.

Format
The course consists of a 3-hour lecture. An accompanying 2-hour hands-on computer workshop, instructor-led, is also available (see below). Workshop attendees will receive hands-on experience with NCBI resources and will have the opportunity to apply these resources to their specific interests and/or research areas.

• Lecture
  The lecture is open to all principal investigators, professional staff, postdoctoral fellows, and graduate students. You may register only for the lecture OR for both the lecture and one of the computer workshop sessions.
  
• Hands-on Workshop
  You must register for the Field Guide lecture in order to be eligible to register for one of the offered workshops. All workshops offered are identical in content. Choose the workshop that best fits your schedule. Workshop space is limited due to the number of computer laboratories available. Register early to insure a place. Every attempt will be made by both Purdue Libraries and NCBI to enroll all interested. A waiting list will be maintained.

Registration
Registration is required for both the Field Guide lecture and workshop.

Instructors
Peter Cooper, Eric Sayers

Times
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Description
The goal of the Gene Ontology (GO) project is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes. This GO demonstration lecture and workshop is designed to teach users about what ontologies are and how they can be used to improve data integration in biology. Both lecture and workshop attendees will learn how to use GO, its browser (AmiGO) and ontology editor (DAG-Edit). The workshop is a hands-on, annotation laboratory which extends the practice examples given in the lecture into a practical hands-on annotation workshop. The workshop will enable attendees to manipulate GO to make their own GO subsets.

Audience
Registration for the lecture is unrestricted. No prior experience is required. The course is designed for novice and experienced graduate students, postdoctoral fellows and faculty/professional staff researchers, regardless of professional discipline. Although annotation experience is not necessary, workshop registrants should have some background knowledge of GO in order to receive the maximum benefit from the workshop.

Format
The course consists of a 2-hour lecture OR a 4-hour hands-on workshop which duplicates the content of the lecture (see below). Lecture attendees may bring their wireless-access enabled computer laptops and follow the lecturer, as conditions permit.

• Lecture
  Registration for the lecture is unrestricted and open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. If you are interested in learning about GO and what it can do, register for the lecture. An open consultation period with EBI instructors for lecture participants will be available beginning at 3:30 PM Friday, May 20 immediately following the last EBI lecture for the week.
  
• Hands-on Workshop
  If you want to practice annotation, making your own GO subsets, register for the workshop. The workshop overlaps the lecture content, but differs in that it provides hands-on practice of GO annotation as well as providing the opportunity to create your own GO subsets. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor availability! Register early. Registration will be "first come - first serve." A waiting list will be maintained if necessary.
  

Registration
Registration is required for both the Gene Ontology lecture and workshop.

Instructors
Emily Dimmer

Times
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Description
Replacing LocusLink, the NCBI Entrez Gene resource provides a unified search environment to gene-related information identified by sequence and/or chromosome information. It can be viewed as a centralized gene-related portal, linking to resources related to any given gene, including its sequence, RNA and protein-related information. Gene QuickStart focuses on how to use Gene to locate information for individual genes including its DNA and mRNA sequences, and exon-intron locations. You will also learn how to determine whether SNPs of the gene’s coding region are known to alter protein product function.

Audience
No prior experience with any NCBI resources, including LocusLink or Gene, is required. The course is designed for novice and experienced graduate students, postdoctoral fellows and faculty/professional staff researchers, regardless of professional discipline, who have a need for a more focused instruction on locating resources related to a given gene than provided in the Field Guide course.

Format
The course consists of a 90 minute overview demonstration-style lecture. An accompanying 60 minute, hands-on computer workshop is also available on a limited basis. A 30 minute individual consultation period will be provided by the NCBI instructors for workshop attendees.

• Lecture
  Open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. You may register only for the lecture OR for both the lecture and one of the computer workshops sessions.
  
• Hands-on Workshop
  You must register for the companion Gene QuickStart lecture in order to be eligible to register for one of the two offered workshops. Both workshops offered are identical in content. Workshop space is limited to two sessions only due to NCBI instructor availability. Register early to insure a place. A waiting list will be maintained if necessary.

Registration
Registration is required for both the Gene QuickStart lecture and workshop.

Instructors
Medha Bhagwat

Times
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Keynote Presentation

Description
The publication of the initial sequence and analysis of the human genome in February of 2001 marked the beginning of a new era for modern biology. Since that time, the impact of having the human sequence in hand has been nothing short of tremendous. What has become obvious in these last few years is that, regardless of one¹s specific area of endeavor, one of the critical keys to conducting cutting-edge biological research in this new era lies in the ability to combine both laboratory- and computationally-based approaches in a synergistic manner, allowing the investigator to better design experiments and to facilitate the analysis of larger and larger experimental data sets. Unfortunately, despite its great power and potential in solving biological problems, the realm of bioinformatics still remains terra incognita for many biologists. This lecture will focus on current themes in the area of bioinformatics and their applicability to both basic and clinical research.

Instructors
Andreas D. Baxevanis - Keynote Speaker

Times
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Description
A lecture only, Introduction to BioMart will focus to how BioMart can be used by laboratory-based, non-programming, researchers. BioMart is a simple, distributed data integration system with powerful genomic-based query capabilities. Currently, 13 different genomes are available for searching through UniProt, Macromolecular Structure Database (MSD), Ensembl, Vega and dbSNP. The aim of BioMart is to provide a practical, personal data mining tool for lab scientists with or without programming skills.

Results can be grouped and refined under many available user-defined criteria and saved to the hard drive of your personal computer. Available remotely over the Internet, all of its software, including an easy to install BioMart website, is also available for local installation. The BioMart software is completely Open Source and freely available to anyone without restrictions.

Audience
Registration unrestricted. This lecture is primarily aimed towards non-programming Purdue University faculty, staff, (including visiting faculty and staff) and graduate students, who would like to learn how BioMart can be used within their own research. However, programmers may also register for the Using BioMart lecture which will focus to how BioMart can be used by laboratory-based researchers. If you are programmer and would like to know more about BioMart, what it is and how it can be managed at the system administrator level, you may also register for Using BioMart programming workshop.

Format
Two hour demonstration lecture only. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor availability! Register early. A waiting list will be maintained if necessary.

Registration
Registration is required for the Introduction to BioMart lecture.

Instructors
Arek Kasprzyk

Times
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Description
EMBOSS is a sequence analysis package consisting of over 200 applications.There are 22 applications that can be applied to the alignment of two or more sequences. In addition to applications for creating alignments, such as dot plots, local, global and multiple alignment, there are a variety of programs for determining consensus and variation within existing alignments.

61 applications have been written with the purpose of providing analysis for nucleic acids. Composition, codon usage and repeat motifs may all be established using this portion of the software. Other analyses such as restriction mapping, primer design, translation and mutation may also be performed.

Protein analysis is a further feature within the EMBOSS suite of bioinformatics applications. There are 41 protein analysis programs currently available for analysis of amino acid sequences including secondary structure prediction, pattern recognition and composition analysis.

12 separate utilities to create and index databases are also modules within the EMBOSS suite, enabling you to build and query your own sequence repositories. Further programs contribute to the general analysis content of the suite.

This lecture will look at some of these applications and their application to biological problems. It will also demonstrate a variety of interfaces to access these programs.

Audience
No prior programming experience is required. This session is aimed towards non-programming Purdue University faculty, staff, (including visiting faculty and staff) and graduate students who would like to learn what EMBOSS is and how it can be used within their individual research efforts. If you are programmer and would like to know more about programming with EMBOSS, you may also register for the Programming with EMBOSS workshop.

Format
The course consists of a 2-hour lecture open to all principal investigators, professional staff, postdoctoral fellows, and graduate students. An open consultation period with EBI instructors for lecture participants will be available Friday, May 20 immediately following the lecture.

Registration
Registration is required for the Introduction to EMBOSS lecture.

Instructors
Peter Rice

Times
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Description
The course focuses on developing strategies for integrating DNA and protein sequence information from different database resources at NCBI. During the demonstration lecture, the instructor will walk the audience through an analysis of an uncharacterized gene which will include locating the gene within a DNA sequence, predicting the function of its implied protein product, seeking similar proteins through BLAST sequence similarity searches and finally locating a 3D modeling template. For those taking the workshop, a similar exercise will be performed hands-on, but with a different genomic sequence.

Audience
Basic familiarity with the steps and processes involved in BLAST sequence searching is required, either through registration for the BLAST QuickStart demonstration-style lecture offered on Monday, May 16 or from prior experience.

Format
The course consists of a 90 minute overview demonstration lecture. An accompanying 60 minute, hands-on computer workshop is also available on a limited basis. A 30 minute individual consultation period will be provided by the NCBI instructors for workshop attendees.

• Lecture
  Open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. You may register only for the lecture OR for both the lecture and one of the computer workshops sessions.
  
• Hands-on Workshop
  You must register for the companion Making Sense of DNA and Protein Sequences lecture in order to be eligible to register for one of the two accompanying workshops. Both workshops offered are identical in content. Workshop space is limited to two sessions only due to NCBI instructor availability. Register early to insure a place. A waiting list will be maintained if necessary.

Registration
Registration is required for both the Making Sense of DNA and Protein Sequences lecture and workshop.

Instructors
Medha Bhagwat

Times
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Description
EMBOSS is an open source software suite that includes over 200 applications for in silico analysis of biological problems. Over 22 applications can be applied to the alignment of two or more sequences, including applications for creating alignments such as dot plots, local, global and multiple alignment and several programs for determining consensus and variation with existing alignments. EMBOSS also contains 61 nucleic acid alignment applications, 41 protein analysis applications and 12 utilities to create and index databases.

There are two main EMBOSS libraries, Nucleus and Ajax. All EMBOSS programs are written in the EMBOSS language, which is essentially C with a few exceptions used from C++. The source code is available to use within your own scripts and workflows and as an open source project. Suitable contributions of applications not yet represented in the suite are welcome. This programming hands-on workshop will look at some of the characteristics of the EMBOSS language and its incorporation into an EBI workflow, Taverna.

Audience
Purdue University faculty, staff, (including visiting faculty and staff) and graduate students with at least a basic understanding of the C programming language. (C++ experience is not required). If you are a non-programmer and would like to know more about EMBOSS, what it is and what it can do for your research efforts, register for the Introduction to EMBOSS lecture instead.

Format
The course consists of a 4-hour hands-on programming workshop. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor and computational equipment availability! Register early. A waiting list will be maintained if necessary.

Registration
Registration is required for the Programming with EMBOSS workshop.

Instructors
Peter Rice

Times
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Description
The EBI has a large proteomics research and service group. This lecture and workshop are designed to introduce participants to the large variety of EBI proteomic databases, the data they contain and the ways of working with them to enhance your protein research. InterProScan is a tool to allow you to predict protein function by searching your protein or nucleotide sequence against the patterns, motives and Hidden Markov Models (HMM) within the InterPro database which is a consolidated proteomic database resource containing PROSITE, Pfam, PIRST, Prints, SuperFamily, ProDom, CATH, TigerFAMS, SCOP, MSD (Molecular Structure Database), Gene3D and PANTHER. A BLAST can then be performed against UniProt, the single protein sequence repository created in 2003 to combine the resources of SwissProt, TrEMBL and PIR. Also to be introduced during this course will be the protein-protein interaction database, IntAct, and PRIDE (PRotemic IDEntifications) public database, a new EBI repository of identification data from large-scale proteomic projects such the Human Proteome Project (HuPo) and the Plasma Proteome Project.

Audience
No prior experience is required. Basic familiarity with the steps and processes involved in BLAST sequence searching, either through registration for the NCBI BLAST QuickStart demonstration-style lecture offered on Monday, May 16 or from prior experience is helpful, but not necessary.

Format
The course consists of a 2-hour lecture OR a 4-hour hands-on workshop which duplicates the content of the lecture (see below). Lecture attendees may bring their wireless-access enabled computer laptops and follow the lecturer, as conditions permit.

• Lecture
  Registration for the lecture is unrestricted and open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. If you are interested in learning about GO and what it can do, register for the lecture. An open consultation period with EBI instructors for lecture participants will be available beginning at 3:30 PM Friday, May 20 immediately following the last EBI lecture for the week.
  
• Hands-on Workshop
  The workshop considerably duplicates the content of the lecture, but differs in that it provides hands-on practice of the lecture demonstration examples. Both workshops are identical. Chose the one that best fits your schedule. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor availability! Register early. Registration will be "first come - first serve." A waiting list will be maintained if necessary.

Registration
Registration is required for either the Ensembl lecture or workshop.

Instructors
Sandra Orchard

Times
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Description
SRS is a powerful unified query interface to over 150 world-wide databases related to nucleotide and protein sequence information. Databanks developed at NCBI, EBI and others may be searched simultaneously or chosen from a library of databases organized into categories such as literature (journal, clinical, patent), nucleotide, protein, ontology, cell lines, pathways and more. SRS enriches the original data with html hyper-linking. This feature enables the user to not only retrieve data within any given database, but also any conceptually related database for which the searcher may not have been aware contained information relevant to the query. In addition to sequence retrieval, EBI’s SRS implementation has incorporated several analysis options which offer the opportunity to analyze individual sequences using various tools or conduct the same sequence homology search across different databases.

Audience
No prior experience is required. Basic familiarity with the steps and processes involved in BLAST sequence searching, either through registration for the NCBI BLAST QuickStart demonstration-style lecture offered on Monday, May 16 or from prior experience is helpful, but not necessary.

Format
The course consists of a 2-hour lecture OR a 4-hour hands-on workshop which duplicates the content of the lecture (see below). Lecture attendees may bring their wireless-access enabled computer laptops and follow the lecturer, as conditions permit.

• Lecture
  Registration for the lecture is unrestricted and open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. It will focus on a particular example, and then proceed through a variety of options for sequence retrieval and data analysis. An open consultation period with EBI instructors for lecture participants will be available Friday, May 20 immediately following the lecture.
  
• Hands-on Workshop
  The workshop duplicates the content of the lecture, but differs in that it provides hands-on practice of the lecture demonstration examples. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor availability! Register early. Registration will be "first come - first serve." A waiting list will be maintained if necessary.

Registration
Registration is required for either the SRS lecture or workshop.

Instructors
Lisa Mullan

Times
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Description
This course focuses on protein structural analysis. It covers how to visualize and annotate 3D protein structures with NCBI’s 3D viewer, Cn3D, identify conserved domain(s), search for proteins with similar domains, explore a 3D modeling template, and find distant sequence homologs that may not be identified through a BLAST similarity search.

Audience
Basic familiarity with the BLAST sequence searching process is advisable. Although it is not necessary to have prior experience using BLAST, the BLAST QuickStart module will provide the foundation for the strategies employed in this mini-course module.

Format
The course consists of a 60 minute overview demonstration-style lecture. An accompanying 90 minute, hands-on computer workshop is also available on a limited basis. Individual consultation is available to workshop attendees following the workshop.

• Lecture
  Open to all Purdue University faculty, staff, (including visiting faculty and staff) and graduate students. You may register only for the lecture OR for both the lecture and one of the computer workshops sessions.
  
• Hands-on Workshop
  You must register for the companion Structural Analysis QuickStart lecture in order to be eligible to register for one of the two accompanying workshops. Both workshops offered are identical in content. Workshop space is limited to two sessions only due to NCBI instructor availability. Register early to insure a place. A waiting list will be maintained if necessary.

Registration
Registration is required for both the Structural Analysis QuickStart lecture and workshop.

Instructors
Medha Bhagwat

Times
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Description
BioMart, a simple, distributed data integration system with powerful genomic-based query capabilities, is based upon distributed data warehousing ideas. Currently, it has been applied to the following EBI data sources: UniProt, Macromolecular Structure Database (MSD), Ensembl, Vega and dbSNP. Specifically for use with large datasets, it is the database upon which the Ensembl query tool Ensmart has been based. The aim of BioMart is to provide a practical data mining framework for lab scientists and computer savvy bioinformaticians, alike. It provides users with the ability to conduct fast, powerful queries against BioMart datasets using either web, graphical, or text based applications, or programmatically using software libraries written in Perl and Java. For data providers, the system simplifies the task of integrating their own data with other datasets hosted on a network. Available remotely over the Internet from the main EBI or Ensembl webpages, all of its software, including an easy to install BioMart website, is available for local installation. The BioMart software is completely Open Source and freely available to anyone without restrictions. This workshop practical will act as an introduction to the system and to the basic management of the system from an administrator level.

Audience
A basic understanding of computer programming is required. This hands-on workshop is aimed towards any Purdue University faculty, staff, (including visiting faculty and staff) and graduate, who would like to program with BioMart within their own research groups and/or to administrate the resource for their non-programming colleagues at Purdue. If you would like to know more about BioMart, what it is and what it can do for your research efforts, but have no exposure to computer programming, register for the Introduction to BioMart lecture instead.

Format
Four hour hands-on programming workshop only. Individual consultation with the EBI instructor will be available to workshop participants immediately following the workshop. Workshop computer space is limited to a single session due to instructor and computational equipment availability! Register early. A waiting list will be maintained if necessary.

Registration
Registration is required for the Using BioMart workshop.

Instructors
Arek Kasprzyk

Times
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