Description
The European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK, grew out of the pioneering work by the European Molecular Biology Laboratory (EMBL) to provide biological databases to the research community. Today EBI is a centre for research and services in bioinformatics, housing a wide variety of databases of biological data, including genomic, proteomic, biochemical, structural, interaction, and expression data, amongst others. In addition, the EBI provides a toolbox of bioinformatics software and search engines with which to analyse and collate the wealth of biological data. The EBI training workshop will provide a thorough grounding in a selection of fundamental EBI genomic and proteomic databases, including the appropriate analysis software.

Description
The Microarray team at the EBI provides public resources for storing, managing and analyzing microarray data, and is a public, online repository for microarray data that conforms to the Microarray Minimum Information for Microarray Experiment (MIAME) standards. ArrayExpress stores both normalized and well-annotated raw data from 40,000 hybridization studies in more than 70 species. Data can be submitted on-line, and password protection to pre-publication data is provided for authors and reviewers. This course will examine how to query data in ArrayExpress, deposit data, and give yourself and other microarray community members access to your data at the level of the experiment or the gene. 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 1-hour lecture OR a 2-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 Stanford University faculty, staff, (including visiting faculty and staff) and graduate students. An open consultation period with EBI instructors for lecture participants will be available.
  
• 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
Helen Parkinson

Times
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Description
The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) group is one of the three partners in the worldwide Protein Data Bank (wwPDB, http://www.wwpdb.org/), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data. Since its inception in 1996, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean-up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. The MSD has developed different query systems in order to allow users to interact with the database and retrieve clean, consistent data for their own use. In addition, the MSD has also developed new algorithms and visualization methods to help analysis of structures and improved the deposition pipeline with the latest release of AutoDep4.0 (http://www.ebi.ac.uk/msd-srv/autodep4/), an in-house archival and web-based structure deposition tool. This workshop will introduce participants to various services offered by the MSD that can help in soling research problems.

Audience
No prior experience is required.

Format
The course consists of a 1-hour lecture OR a 2-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 Stanford University faculty, staff, (including visiting faculty and staff) and graduate students. An open consultation period with EBI instructors for lecture participants will be available.
  
• 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
Sameer Velankar

Times
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Description
Reactome is a collaborative project between the EBI and the Cold Spring Harbor Laboratory, USA, consisting of a curated knowledgebase of biological processes described in terms of reactions, pathways, macromolecules, small molecules, complexes and catalyst activities. These processes include both well-defined metabolic pathways, such as glycolysis, as well as a diverse range of other pathways, such as signalling pathways and cell cycle regulation. The Reactome web interface provides a textbook-like view of cellular processes, plus features for keyword searching, integrating expression data and generating protein-protein interactions. This course describes the underlying concepts behind Reactome, and explores the main features of the web interface using hands-on exercises. In addition, participants will be guided through the process of setting up their own Reactome site, and shown how to use the curation tools available.

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 Stanford is encouraged to attend.

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

Registration

Instructors
David Croft

Times
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Description:
EBI Web Services, such as SOAP (Simple Object Access Protocol), is an integration technology that provides information retrieval and data analysis tools for use with multiple databases, without the need for manual searching through a web browser or for installing and maintaining databases in-house. Moreover, information retrieval and analysis are linked, enabling the combination and manipulation of search results. Using these technologies, programmers can build complex applications in their language of choice (such as Java, Perl, VB, C#, C++, Python, Ruby, R and PHP), with data access directly from and to your code. As a result, you can submit large and complex jobs straight from your data pipeline with all of the results being returned directly to your software for processing at the next stage. The number of tools and databases at the EBI that have Web Services access is now in double figures, making the adoption of this technology very advantageous for any laboratory involved in data-intensive research. You can retrieve data from multiple EBI databases using the WSDbfetch web service; and you can make use of sequence similarity tools such as Blast, Fasta and MPsrch and perform multiple sequence alignments using ClustalW, T-Coffee or MUSCLE. You can also explore the InterPro protein families and domains database using InterProScan and perform powerful queries over 40 different biological ontologies via the ontology lookup service. In this lecture, the EBI Web Services will be demonstrated, providing an overview of what the individual Web Services can offer.

Audience:

Format: The course consists of a 1-hour lecture/demonstration. 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:

Instructor
Phil Jones

Times
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Description
Ensembl is a joint project between EBI and the Sanger Institute, which provides automatic annotation of large genomes and the relationships among them. Ensembl is rapidly growing, and currently contains annotation for over 20 species (including human, chimpanzee, Rhesus macaque, mouse, rat, dog, cow, opossum, chicken, zebrafish, among others). Ensembl also imports the manually curated data from other model organisms to use as comparisons (i.e. Drosophila from FlyBase, C. elegans from WormBase and yeast from SGC). Ensembl has a unique gene analysis pipeline with each piece of genomic information predicted and then supported by biological evidence. Additionally, ESTs, mRNAs, SNPs, proteins and other biological information are mapped to the genomes.
This course 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, BioMart: a "query builder" interface which allows users to specify genomic regions and refine results. BioMart is a simple, distributed data integration system with powerful genomic-based query capabilities. BioMart can generate a number of different types of output, including sequence and tabulated list data. This course will also introduce BioMart, focusing on how it can be used by laboratory-based, non-programming, researchers.

Audience
No prior experience is required. Basic familiarity with the steps and processes involved in BLAST sequence searching 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 Stanford 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 Stanford 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

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: biological process, molecular function, and cellular component. This GO demonstration lecture is designed to teach users about what ontologies are and how they can be used to improve data integration in biology.

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 Stanford 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
This workshop will introduce participants to three major EBI proteomic databases - UniProt, InterPro, IntAct and PRIDE – and explore the wealth of information they contain that can enhance your research. UniProt is a central repository of protein sequence and function created by combining the information in Swiss-Prot, TrEMBL and PIR, while InterPro and IntAct provide free open source data and resources aimed at analysing proteomes and interactomes. InterPro provides information on the function, annotation and classification of proteins by combining the major signature databases from Gene3D, Pfam, PIRSF, Prints, ProDom, Prosite, Smart, SuperFamily, Tigrfams, and PANTHER into a unified protein resource. InterPro then adds structural annotation by mapping individual proteins to PDB, MSD, CATH, SCOP, ModBase and SwissModel, as well as functional annotation through GO mapping, literature summary and references, and links to several external databases (Pandit, CAZy, Merops, IUPHAR, COMe, Cluster, Blocks, and Prosite doc). IntAct provides a comprehensive, annotated data resource for protein interactions derived from literature curation and through direct submissions. The interactions can be viewed individually, or as part of an interaction network, using GO mappings to help define the proteins involved in such networks.

Audience
No prior experience is required. Basic familiarity with the steps and processes involved in BLAST sequence searching is helpful, but not necessary.

Format
The course consists of a 2-hour hands-on workshop. Lecture attendees may bring their Stanford registered wireless-access enabled computer laptops and follow the lecturer, as conditions permit.

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
Jennifer McDowall

Times (Monday and repeats on Tuesday)
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Description
PRIDE provides free open source data and resources aimed at analysing proteomes. PRIDE is a repository of protein identification data from large-scale proteomic projects, such the Human Proteome Project (HUPO) and the Plasma Proteome Project. This tutorial is suitable for both biologists and bioinformaticians, and will focus on the type and organisation of annotated data, the different query methods possible, understanding the different visualisations of the data, as well as exploring the multiple links and cross-references available between the different databases covered and to external databases. In addition, the tutorial will provide information on the submission processes for IntAct and PRIDE.

Audience
No prior experience is required. Basic familiarity with the steps and processes involved in BLAST sequence searching is helpful, but not necessary.

Format
The course consists of a 1-hour lecture OR a 1-hour hands-on workshop which duplicates the content of the lecture (see below). Lecture attendees wotj Stamfprd registered computers may bring their wireless-access enabled computer laptops and follow the lecturer, as conditions permit.

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. 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 PRIDE lecture or workshop.

Instructors

Phil Jones

Times
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Description
This mini-course deals with the identification of a disease gene using
NCBI's human genome assembly. The reference genome assembly, along with
integrated maps, literature, and expression information comprises a
powerful discovery system for exploring candidate human disease genes.
We will start with EST sequences that might have been obtained from a
patient, identify the gene(s) expressing them, download their sequences,
determine the exon-intron structure and identify known single nucleotide
polymorphisms (SNPs) in the ESTs, if any, that may contribute to the
disease phenotype.

The course will emphasize the integration of NCBI tools such as BLAST,
Map Viewer, Single Nucleotide Polymorphism Database (dbSNP), and Online
Mendelian Inheritance in Man (OMIM).

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. An individual consultation period will be provided by the NCBI instructors for workshop attendees.

• Lecture
  Open to all Stanford 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
  The workshop is highly recommended for the mini-courses. You must register for the companion NCBI Mini Courselecture in order to be eligible to register for the workshop. Workshop space is limited. Register early to insure a place. A waiting list will be maintained if necessary.

Registration
Registration is required for all lectures and workshops.

Instructors
Medha Bhagwat

Times
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Description
This mini-course focuses on determining what is known about a disease
and the gene associated with it. It also elucidates the biochemical and
3-D structural basis for the phenotype caused by a single nucleotide
polymorphism that results in an altered protein.
The course will emphasize the integration of resources such as Entrez
Gene, Single Nucleotide Polymorphism Database (dbSNP), GeneTests, Online
Mendelian Inheritance in Man (OMIM), Conserved Domain Database (CDD),
and Cn3D.

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. An individual consultation period will be provided by the NCBI instructors for workshop attendees.

• Lecture
  Open to all Stanford 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
  The workshop is highly recommended for the mini-courses. You must register for the companion NCBI Mini Courselecture in order to be eligible to register for the workshop. Workshop space is limited. Register early to insure a place. A waiting list will be maintained if necessary.

Registration
Registration is required for all lectures and workshops.

Instructors
Medha Bhagwat

Times
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Description
This mini-course will provide an introduction to protein sequence
analysis, beginning with the prediction of a gene within a DNA sequence
and ending with a model 3-D protein structure.
Topics to be covered include:

A. Exon prediction and the generation of a protein sequence
B. Protein function prediction
C. Identification of the characteristic domains and motifs in the
protein
D. Mapping of the protein sequence onto the structure of a protein with
similar sequence

The course will also address how the tools can be applied to the
analysis of a microbial DNA sequence.

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. An individual consultation period will be provided by the NCBI instructors for workshop attendees.

• Lecture
  Open to all Stanford 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
  The workshop is highly recommended for the mini-courses. You must register for the companion NCBI Mini-Course lecture in order to be eligible to register for the workshop. Workshop space is limited. Register early to insure a place. A waiting list will be maintained if necessary.

Registration
Registration is required for all lectures and workshops.

Instructors
Medha Bhagwat

Times
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Description

Bob Kuhn
Overview of the UCSC Genome Browser
This presentation will focus on the Genome Browser main display, its
controls, navigation and configuration, as well as the Known Genes track and
its companion modules, the Gene Sorter and Proteome Browser. Finally, the
Custom Track utility for displaying user-generated data on the Browser will
be demonstrated along with the Table Browser, which is used for data
filtering and intersections between tables and custom tracks.

Heather Trumbower
Under the Hood: Using the code behind the browser
The focus of this talk will be using the UCSC source code. This includes how
to obtain the source tree and build it. Important utilities and libraries
will be highlighted, and the sequence formats (nib and 2bit) will be
reviewed. The talk will also cover the basics of setting up a mirror site
and a description of how we document our data processing (makeDocs). If
time allows, the cluster management tool 'parasol' and the Genbank update
process will be reviewed.

Daryl Thomas
Comparative Genomics at UCSC
This presentation will focus on comparative genomics -- the methods and
applications. The motivation supporting comparative genomics and the power
of comparing many species will be reviewed, and simple examples of pairwise
alignments will be followed by chaining and netting. Multiple species
alignments will be briefly described, and examples of their use in
conservation analysis (phastCons), exon prediction (exoniphy), microRna
structure prediction (evoFold), and regulatory potential (RP) will be shown.

Audience
Registration unrestricted.

Format
Two hour demonstration lecture only. Individual consultation with the 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 lecture.

Instructors
Bob Kuhn
Daryl Thomas
Heather Trumbower

Times
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Description
A lecture only, "Accessing and Analyzing Public Data with the Stanford Microarray Database"

Audience
Registration unrestricted.

Format
Two hour demonstration lecture only. Register early. A waiting list will be maintained if necessary.

Registration
Registration is required for the Introduction to this lecture.

Instructors
Catherine Ball, Director of the Microarray Database Group

Times
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Description
Many bioinformatics databases support SOAP or Internet SQL querying. Such services are a boon to researchers who would otherwise be limited to querying these databases via the Web, with the concomitant difficulty in extracting the relevant data into a format more amenable to summarization, such as that provided by spreadsheet programs. A use case will be presented which involves a simple Perl application that queries the MeSH and PubMed databases using SOAP. Its purpose is to characterize what is known about a collection of candidate genes in order to facilitate the optimal selection of genes to be genotyped. The querying tool executes large number of queries whose results are summarized automatically for visual inspection using simple Excel functions. Because this approach (direct querying and data manipulation within Excel) is both simple and generic, it can be applied to many other types of data beyond those provided by NCBI.

Audience
Registration unrestricted.

Format
Two hour demonstration lecture only. Individual consultation with the 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 lecture.

Instructors
Yannick Pouliot

Times
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Description
A key step in understanding genome data is being able to view and use it in the context of the full metabolic and regulatory network of an organism. The online BioCyc collection presents pathway/genome databases for over two hundred organisms along with tools for interacting with individual organisms or comparing across many organisms. These databases can also be worked with via the Pathway Tools software package, which is both a navigation tool and can generate a database de novo from any annotated genome. This lecture will introduce the concept of the pathway/genome database via the BioCyc collection, then demonstrate the additional capabilities of the Pathway Tools software package, including discussion of what is involved in making a database for your own organism of interest.

Audience
Registration for the lecture is unrestricted. This course is open to everyone from beginners to those who are looking for more advanced tools to understand one or many organisms.

Format
The course consists of a 90-minute lecture, with opportunities for Q&A throughout. The instructor will also be available for additional Q&A following the lecture period.

Registration

Instructors
Alexander Shearer

Times
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Description

Audience

Format

Registration

Instructors

Times
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