SoyBase.org News

SoyBase News

David Grant — 2009-05-21 12:39:17

Try the new SoyBase whole genome sequence browser

SoyBase News

Andrew Denner — 2009-05-22 13:41:36

The SoyBase RSS feed is now available. See here for details.

SoyBase News

David Grant — 2008-12-08 12:00:00

The Glyma1.0 chromosome-based assembly and annotation of soybean is now available, replacing the preliminary contig-based assembly and annotation.

SoyBase News

David Grant — 2008-07-30 12:00:00

A table is now available to convert the soybean linkage group names to chromosome numbers. The table was compiled by Perry Cregan's group at the USDA-ARS Soybean Genomics and Improvement Laboratory.

SoyBase News

David Grant — 2008-08-15 12:00:00

The SoyBase and Soybean physical map websites have undergone a user interface upgrade. Please tell us your impressions. You can contact us HERE

SoyBase News

David Grant — 2008-08-15 12:00:01

SoyBase Soybean ontologies are available from the SoyBase site under "Soybean Ontologies" in the SoyBase sub-nav bar. These ontologies cover soybean growth and development. Input from the community is actively encouraged.

SoyBase News

dgrant — 2009-10-02 10:43:15

Soybean data at PLEXdb. PLEXdb is now home to 13 more soybean data series imported from NCBI-GEO. There are now 16 publicly visible experiments associated with the Soybean Affymetrix chip.

SoyBase News

dgrant — 2010-03-01 16:19:34

BARCSOYSSR 1.0, a collection of 33,065 potential SSRs identified by Qijian Songand Perry Cregan from the Wm82 genomic sequence has been released. These SSRs arenow available as a track in the SoyBase Genome Browser. The whole dataset is availablefor download.

SoyBase News

dgrant — 2010-03-18 13:59:07

Explore soybean metabolic pathways using the SoyCyc metabolic pathway interface.This interface allows users to explore soybean metabolic pathways that have beenelectronically annotated with the Glyma 1.01 gene calls from JGI.

SoyBase News

dgrant — 2010-04-12 13:46:59

We have added a selection of preconfigured views to the SoyBase Genome Browser.Choosing one of the Example Views in the Search section at the top of the page will turn on a set of related tracks in the viewer. These examples show some of the kinds of data available in the genome viewer and can be used as a starting point forconstructing a customized set of tracks.

SoyBase News

dgrant — 2010-07-13 10:43:56

The Soybean Genetics Newsletter has ceased publication. An archive of the site has been set up at SoyBase and is accessible from the Soybean Genetics Newsletter link on the Resources page.

SoyBase News

dgrant — 2010-05-25 17:26:14

Information about the gene models has been updated with improved annotations and enhanced sequence browser views and text reports. Additionally it is now possible to download the mRNA, CDS or predicted protein sequences for a gene model and all of its splice isoforms from the text page returned by clicking on a gene model name in the SoyBase Genome Browser.

SoyBase News

dgrant — 2010-08-17 14:24:47

A collection of photos taken by Rich Wilson at the 13th Biennial Molecular & CellularBiology of the Soybean held in Durham, NC in August 2010 has been posted.

SoyBase News

dgrant — 2010-09-03 14:13:58

A Progress Report has been completed by Rich Wilson and DavidGrant based onresponses to a survey sent out in early 2010. A PDFversion of the report, SoyGenStratPlan2008-2012-Accomplishments v1.6, isavailable.

SoyBase News

dgrant — 2010-09-28 13:39:57

A new whole genome display option has been added to the BLAST tool at SoyBase. When chosen, the results of the BLAST are shown for all chromosomes with links to individual zoomed views in the SoyBase sequence viewer.

SoyBase News

dgrant — 2010-10-14 14:34:09

The first in a series of tutorials on SoyBase and soybean genetics and genomics has been posted. This video will walk you through the needed supplies and proper methods in soybean cross-pollination.

Soybean Genomics Research: A Strategic Plan for 2012-2016

David Grant — Mon, 01 November 2010

A document outlining Soybean Genomics Research: A Strategic Plan for 2012-2016 has been released. Word and PDF versions are available here.

Soybean Breeders Workshop presentations posted

David Grant — Mon, 28 February 2011 16:03:20 -0600

PDF files of the presentations made at the 2011 Soybean Breeders Workshop (2/21-23/2011 in St. Louis, MO) have been added to SoyBase. PDF files of the 2010 presentations are also available, and we expect to continue to post similar files from future Workshops.

Improved searching at SoyBase

David Grant — Thu, 05 May 2011 16:25:25 -0500

We have reworked and expanded the search capabilities for SoyBase. The new search page (SoyBase -> Search menubar entry or here) allows the submission of terms in one or more categories. The search results page shows the number and types of data in SoyBase that relate to the search terms, with links from this page to the complete search results. The examples shown on the search page can be used for testing by clicking on the term.

MTP for Wm82 physical map

David Grant — Thu, 05 May 2011 16:29:40 -0500

A Minimum Tiling Path (MTP) for the Wm82 BAC-based physical map has been developed by Jungmin Ha and Scott Jackson (Purdue University). A track for this MTP is available in the SoyBase genome sequence browser.

Improved data downloading from SoyBase

David Grant — Thu, 05 May 2011 16:30:31 -0500

A unified downloads page has been developed where various collections of genetic and sequence data can be retrieved. Please let us know if there are other data types or subsets that you would like added.

GO terms updated

David Grant — Thu, 05 May 2011 16:31:59 -0500

The Gene Ontology (GO) terms associated with the Wm82 gene calls are being updated. The gene calls associated with enzymes involved in metabolism have been revised, and we expect the remainder to be finished soon.

A Strategy for Prioritizing Research Goals and Outreach Plans to Reduce Soybean Production Losses Caused by Stink Bugs and Related Insect Pests

David Grant — Thu, 12 May 2011 09:59:03 -0500

In March 2011 a group of scientists met to develop a research plan to address the emerging problem of a complex of pod-attacking stink bugs. A Strategic Research Plan was produced.

SoyBase and other plant databases at the Plant Biology 2011 Outreach Booth

David Grant — Thu, 04 August 2011 10:14:06 -0500

If you plan to be at ASPB (Aug. 6-10), please stop by and see SoyBase and other plant databases at the Plant Biology 2011 Outreach Booth.

Improved Genetic Maps Display

David Grant — Mon, 14 November 2011 08:54:57 -0600

The number of QTL on the genetic maps has dramatically increased as the SoyBase staff continues to incorporate QTL experiments from the literature. This has resulted in displays that are increasingly crowded and potentially difficult to use. To address this we have split the QTL into 4 classes (seed composition & yield, disease & stress, plant architecture, and other traits) with each of these classes presented as a separate column in the CMap genetic map displays. We hope that this will enhance the usefulness of the genetic maps. As always, comments on these changes are encouraged.

Soybean Mutant Finder Field Day

David Grant — Thu, 05 January 2012 13:15:46 -0600

The 1st Soybean Mutant Finder Field Day will be held in late July, 2012 at the University of Minnesota. Participants will view fast neutron-derived mutant plants growing in the field and can request seed of those that may be of research interest. A tutorial on the gene knockout-related parts of SoyBase will be presented. Contact Carroll Vance or Bob Stupar for more information.

Soybean Genomics Research Strategic Plan Updates

David Grant — Wed, 01 February 2012 15:27:35 -0600

Progress made by the soybean community on the 2012-2016 Soybean Genomics Research Strategic Plan is being compiled by George Graef, Katy Rainey and Rich Wilson. Please see the Strategic Plan website for details on how to contribute to the report.