ASPB 2012 Booth
Visit a collection of Plant Genomics databases and projects with resources for sequenced genomes, ontology development, genetic mapping, functional annotation of genes, mutants and phenotypes, genetic diversity, and bioinformatics tools. Representatives from the projects indicated below will be present to demonstrate tools for cutting-edge genomics and genetics research and to answer questions.
You can find us at Booth #200
- 1 Genomic Tools Minisymposium
- 2 Plant Genome Resources Outreach Booth
- 2.1 Projects with a Representative On Site
- 2.2 Projects without a Representative On Site (Brochures available!)
- 2.3 Acknowledgements
Genomic Tools Minisymposium
Plan to attend the Genomic Tools Minisymposium Sunday, July 21, 3:45 - 5:30 PM
Plant biology researchers increasingly rely on databases and other informatics resources to organize, integrate and provide access to the flood of plant biology data now available. We will present the latest developments, data and tools for several important plant informatics resources. Presentations:
- Jason Williams - iPlant
- Doreen Ware - KBase
- Shelby Bidwell - Medicago truncatula @ JCVI
- Eva Huala - TAIR/IAIC transition
- Joshua Stein - Gramene
- Jeremy Edwards - Sol Genomics Network
- Kate Dreher - Plant Metabolic Network
Plant Genome Resources Outreach Booth
Projects with a Representative On Site
Schedule of Projects with a representative present at the booth
See Gramene's web page for more information: http://www.gramene.org
The Gramene database is a comparative plant genomics platform. The database allows researchers to carryout online data analysis, hypothetical modeling or confirmation of lab based findings using both forward and reverse genetics approaches to find genes, proteins, phenotypes (mutants and QTLs), function(s), gene-gene interaction(s), metabolic pathways and polymorphisms in a genomic region of interest. It also allows researchers to make comparisons across genetic maps, genomes, genes and gene families and provides a mechanism to find candidate genes associated with phenotype and/or functional characteristics by way of whole genome alignments and synteny views.
An overview of the Gramene comparative genomics database as well as latest developments and future plans will be presented by Joshua Stein during the Genomic Tools Minisymposium on Sunday, July 21st at 4:30pm.
Marcela Karey Monaco will be presenting a Gramene poster (P25019 at session #25) and will also be available to answer users queries at the booth throughout the meeting.
Please visit a representative from Gramene at booth #200 on:
For more information please contact: Gramene Feedback
See TAIR's web page for more information: http://www.arabidopsis.org
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with information concerning gene structures, gene product functions, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, useful tools, and members of the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive links from our data pages to other Arabidopsis resources.
- Information on AraCyc, the plant metabolic pathway database connected to TAIR, will be presented in the same workshop.
- Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources.
Come see us at booth #200 on...
For more information please contact: TAIR
Plant Metabolic Network
See PMN's web page for more information: Plant Metabolic Network
The Plant Metabolic Network (PMN) is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases. A central feature of the PMN is PlantCyc, a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.
- Researchers are encouraged to bring their published data to the workshop to learn how to directly enter their exciting findings into all three of these public resources
- Please come visit our Poster # P19014 entitled ‘The Plant Metabolic Network: PlantCyc, AraCyc and 4 NEW metabolic pathway databases for plant research . . . with more on the way'
For more information please contact: PMN Feedback
Solanaceae Genomics Network
See the SGN's web page for more information: http://solgenomics.net
The SOL Genomics Network is a Clade Oriented Database (COD) containing genomic, genetic, phenotypic and taxonomic information for species in the Euasterid clade, including the families Solanaceae (e.g. tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to other important plant model species such as Arabidopsis. SGN is also one of the bioinformatics centers involved in tomato genome sequencing.
One of the major efforts at SGN is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN puts the control over the information in the hands of community experts. As a result, SGN annotations are more up-to-date, and richer with detailed descriptions and gene-to-phenotype cross links, than would otherwise be possible without a large curatorial staff.
For more information please contact: SGN Contact
J. Craig Venter Institute
JCVI can be publicly accessed at http://www.jcvi.org/
The Bio-Array Resource for Plant Functional Genomics
See BAR's web page for more information: http://www.bar.utoronto.ca
The Bio-Array Resource at the University of Toronto is a collection of web-based tools for exploring, visualizing and mining large-scale data sets, primarily from Arabidopsis thaliana but also from several other plant species.
These tools include:
eFP Browser (electronic Fluorescent Pictograph Browser) for painting gene expression and other information onto diagrammatic representations of the particular experimental series from which the data were generated. eFP Browsers are available for Arabidopsis, poplar, Medicago truncatula, rice, barley, soybean, maize, potato and cell.
Expression Angler for identifying co-expressed, anti-correlated, or condition/tissue-specific genes using the "custom bait feature" in 5 of the gene expression data sets from the AtGenExpress Consortium, from our in-house database or from NASCArrays, or several other data sets.
Expression Browser for performing electronic northerns.
Arabidopsis Interactions Viewer for querying a database of almost 80,000 predicted and 28,566 documented protein-protein interactions in Arabidopsis.
Promomer for identifying over-represented n-mer words in the promoter of a gene of interest, or in promoters of co-expressed genes.
ePlant: - A suite of interactive web-based tools that enables users to explore Arabidopsis data from the kilometre to nanometre scale, including natural variation data, organ and cell-type-specific gene expression patterns, subcellular localization, protein-protein interactions, and protein tertiary structures predicted for ~70% of the proteome.
Next-Gen Mapping: - allows for the rapid localization of recessive EMS induced mutations within an F2 mapping population that has been pooled and sequenced en masse using a next-generation sequencing platform.
Please visit a representative from the BAR at booth #200 on:
For more information please contact: Nick Provart (email@example.com)
See our web page for more information http://www.iplantcollaborative.org
Please visit with the iPlant Collaborative during ASPB at Booth #200 during the following dates/times:
See KBase's web page for more information: http://kbase.us
The DOE Systems Biology Knowledgebase (KBase) is a collaborative effort designed to accelerate our understanding of microbes, microbial communities, and plants. It will be a community-driven, extensible and scalable open-source software framework and application system. KBase will offer free and open access to data, models and simulations, enabling scientists and researchers to build new knowledge and share their findings.
Please visit a representative from Gramene at booth #200 on:
Projects without a Representative On Site (Brochures available!)
Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics and breeding. SoyKB handles the management and integration of soybean genomics and multi-omics data (including genomics, transcriptomics, proteomics and metabolomics) along with gene function annotations, biological pathway and trait information. It has many useful tools including Affymetrix probeID search, gene family search, multiple gene/metabolite analysis, motif analysis tool, protein 3D structure viewer and download/upload capacity for experimental data and annotations. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, breeders and consumers.
SoyKB has new innovative tools for soybean breeding including a graphical chromosome visualizer targeted towards ease of navigation for breeders. It integrates QTLs, traits, germplasm information along with genomic variation data such as single nucleotide polymorphisms (SNPs) and genome-wide association studies (GWAS) data from multiple genotypes, cultivars and G.soja. QTLs for multiple traits can be queried and visualized in the chromosome visualizer simultaneously and overlaid on top of the genes and other molecular markers as well as multi-omics experimental data for meaningful inferences.
SoyKB can be publicly accessed at http://soykb.org
Plant Ontology and Plant Trait Ontology
See PO's web page for more information: http://www.plantontology.org
The main objective of the Plant Ontology Consortium (POC) is to develop, curate and share controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages and plant traits. The overall goal is to provide a semantic framework for meaningful cross-species queries across databases. The Plant Ontology (PO) and the Plant Trait Ontology (TO) have been developed with the primary goal to facilitate and accommodate functional annotation efforts in plant databases and by the plant research community at large.
As a part of the PO project, participating databases such as TAIR, NASC, Gramene, and MaizeGDB have been using PO to describe expression patterns of genes and phenotypes of mutants and natural variants.
Come see Poster # P28002: The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa.
For more information please contact: PO Feedback
See MaizeGDB's web page for more information: http://www.maizegdb.org/
MaizeGDB is a community-oriented, long-term informatics service to researchers focused on the crop plant and model organism Zea mays that is funded by the USDA-ARS.
MaizeGDB is currently undergoing a full website redesign (see ) and we would appreciate help and input on making the new site able to meet your research needs!
Of interest to most researchers are the integration of genetics and genomics at MaizeGDB. From the MaizeGDB Genome Browser, cM estimates of genome size are available. Mechanisms to locate loci of interest on the genome are available via the Locus Lookup and Locus Pair Lookup.
Functional genomics tools are also coming along at MaizeGDB with access to the eFP Browser images from the Sekhon et al. Maize Gene Expression Atlas via gene model pages (e.g., ) as well as comparisons and views of the same dataset via MapMan where the data can be visualized online directly.
The Outreach Booth was made possible thanks to volunteer organizers:
- Kate Dreher, PMN
- Marcela Karey Monaco, Gramene