Release Notes March 1, 2004

Summary
  1. New datasets -- eggplant, petunia and pepper ESTs and unigene builds.
  2. International Solanaceae Project Page -- A new version of the whitepaper is available!
  3. Updated toolbar and user interface
  4. Physical map data updated
  5. SGN people directory
  6. SOL Forum mailing list
  7. Bulk download facility
  8. FTP site
  9. Improved search interface

Detailed descriptions

  1. New datasets -- ESTs from Pepper, Petunia and Eggplant added, Potato build updated.

    We have added EST data from pepper, petunia and eggplant. The pepper data was kindly submitted by Prof. Doil Choi of the KRIBB institute (http://www.kribb.re.kr) in Korea; the petunia data was kindly provided by Prof David Clark of University of Florida and Cornell University; and the eggplant data was supplied by Prof. Steven Tanksley of Cornell University. In addition, the potato unigene build was re-run with new sequences kindly provided by Robin Buell of TIGR, USA. We would like to sincerely thank these researchers for making their data available through SGN.

  2. International Solanaceae Project (SOL) page

    The International Solanaceae Project (SOL) page is available at http://sgn.cornell.edu/solanaceae-project/. SOL is an initiative that will create a coordinated network of knowledge about the Solanaceae family aimed at answering two of the most important questions about life and agriculture, namely (1) How can a common set of genes/proteins give rise to such a wide range of morphologically and ecologically distinct organisms that occupy our planet? and (2) How can a deeper understanding of the genetic basis of diversity be harnessed to better meet the needs of society in an environmentally-friendly way? In addition, the page contains information on the meeting in Dulles, Virginia last November and provides downloads for a number of documents, such as the SOL whitepaper draft, information and guidelines for the tomato sequencing project, and transcripts from the Dulles meeting. More information will be available soon, so check back frequently.

  3. Updated toolbar and user interface

    We continue to make improvements to the user interface, hopefully without causing too many disruptive changes. We have improved the toolbar with a better layout of the menus, which are now pull-down menus for easier direct access to the most important pages from any page. In addition, there is now a quick search feature which searches the entire database contents with one simple search. We have re-arranged some of the pages and added more help files and a data overview page (http://sgn.cornell.edu/content/sgn_data.pl). The search page was also overhauled and now has a more functional layout. Please let us know what you think of these changes.

  4. Physical Map Data

    We have integrated the results from almost 700 overgo markers linking the genetic map to the physical map. The results can be viewed graphically at http://sgn.cornell.edu/cview/map.pl?map_id=1&physical=1. The purpose of this project was to develop a tomato physical map anchored to the genetic map and to identify the tomato BAC minimum tiling path for positional cloning and whole genome sequencing. 88,642 BAC clones from a Lycopersicon esculentum cv. Heinz 1706 BAC library with 129,024 clones and roughly 15 genome equivalents generated Unambiguous fingerprints (Arizona Genome Institute). In order to anchor the fingerprinted BACs onto the tomato genetic map, overgo (overlapping oligonucleotide) probes were generated from a total of 1535 sequenced, mapped markers from the current high density tomato map. The map overview page is at http://sgn.cornell.edu/cview/index.pl .

  5. SGN people directory

    SGN has now a directory of people who are actively involved in Solanaceae research. The data can be searched and browsed on-line at http://sgn.cornell.edu/search/direct_search.pl?search=Directory. If you are in the database, a password should have been sent to you that allows you to modify and complete the information in your entry. If you are not yet in the database, you can add yourself at http://sgn.cornell.edu/solpeople/login.pl. You will have to create an account first and then you can add your information.

  6. SOL-Forum mailing list

    To better connect the solanaceae community, a new list has been made available that allows subscribed members to post messages to the list or ask questions to the community. You can subscribe to the list at http://caffeine.sgn.cornell.edu/mailman/listinfo/sol-forum. The scope of the list is solanaceae research and related topics. Please follow the guidelines of the list when posting to make this a useful tool for solanaceae researchers. Unsubscribing is possible at any moment. People who are not subscribe to the list cannot post messages, mainly because this prevents spammers from using the list.

  7. Bulk download facility

    SGN now has a bulk download facility that allows you to download data using lists of clone names, unigene ids, and microarray identifiers. You can specify the information that you would like to download, including associated clone names, associated unigene ids, sequence data and much more. Before downloading the data to your disk in tab delimited or fasta formats, you can browse the data on line. The bulk download is linked from the toolbar on every page and is directly available at: http://sgn.cornell.edu/bulk/input.pl.

  8. FTP site

    SGN now has an FTP site that allows you to download complete datasets. The ftp site is linked from the bulk download page (rightmost tab) and can also be accessed via ftp://ftp.sgn.cornell.edu using a web browser or ftp client. The FTP site is structured into folders that group datasets by type of data. Marker data, EST sequences, unigene sequences and much more can be downloaded. More data will be added to the FTP site in the coming months so check back frequently.

  9. Improved searches

    The database search interface has been improved in the following ways:
    • the different searches are now separated by 'tabs' for better navigation
    • you can now search the unigenes using TIGR identifiers
    • a library search has been added that allows you to search by name, organism, source tissue, development stage, etc.