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This is an automatic announcement that WormBase (http://www.wormbase.org) has just been updated. New releases occur roughly every 2 weeks. The text of the AceDB release notes, which contains highlights of the new data is attached. You can download the full AceDB files from: ftp://ftp.sanger.ac.uk/pub/wormbase/current_release/ New release of WormBase WS110, Wormpep110 and Wormrna110 Mon Sep 22 09:58:44 BST 2003 WS110 was built by Chao-Kung Chen ====================================================================== This directory includes: i) database.WS110.*.tar.gz - compressed data for new release ii) models.wrm.WS110 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS110-WS109.dbcomp - log file reporting difference from last release v) wormpep110.tar.gz - full Wormpep distribution corresponding to WS110 vi) wormrna110.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS110.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) yk2orf.WS110.gz - Latest set of ORF connections to each Yuji Kohara EST clone ix) gene_interpolated_map_positions.WS110.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS110.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS110.gz - for each C. elegans WormPep protein, lists Best blastp match to human, fly, yeast, C. briggsae, and SwissProt & Trembl proteins. xii) best_blastp_hits_brigprot.WS110.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & Trembl proteins. Release notes on the web: ------------------------- http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE Primary databases used in build WS110 ------------------------------------ brigdb : 2003-09-08 - updated camace : 2003-09-09 - updated citace : 2003-09-07 - updated cshace : 2003-09-04 - updated genace : 2003-09-16 - updated stlace : 2003-09-08 - updated Genome sequence composition: ---------------------------- WS110 WS109 change ---------------------------------------------- a 32367165 32367165 +0 c 17780236 17780236 +0 g 17757587 17757587 +0 t 32368413 32368413 +0 n 95 95 +0 - 0 0 +0 Total 100273496 100273496 +0 Wormpep data set: ---------------------------- There are 19936 CDS in autoace, 22168 when counting 2232 alternate splice forms. The 22168 sequences contain 9,672,725 base pairs in total. Modified entries 291 Deleted entries 35 New entries 73 Reappeared entries 2 Net change +40 Status of entries: Confidence level of prediction ------------------------------------------------- Confirmed 4589 (20.7%) Partially_confirmed 9040 (40.8%) Predicted 8527 (38.5%) Status of entries: Protein Accessions ------------------------------------- Swissprot accessions 2413 (10.9%) TrEMBL accessions 18085 (81.6%) TrEMBLnew accessions 1650 (7.4%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22148 (100.0%) Locus <-> Sequence connections (cgc-approved) --------------------------------------------- Entries with locus connection 4460 GeneModel correction progress WS109 -> WS110 ----------------------------------------- Confirmed introns not is a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 6 | -1056 | St Louis | 40 | -710 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 30 | 1 | St Louis | 31 | 0 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ No synchronisation issues There are no gaps remaining in the genome sequence --------------- For more info mail worm <at> sanger.ac.uk -===================================================================================- NOTE: ----- This release (WS110) is the second frozen release followed WS100. It represents a freeze-of-data release and will remain on the Sanger ftp site (ftp://ftp.sanger.ac.uk/pub/wormbase) for the foreseeable future. Also, it will be available from http://ws110.wormbase.org Bioinformaticians seeking to collaborate and share annotation data against the backdrop of a fixed genome sequence may consider working with this release. The next freeze will take place with the release of WS120, approximately in 20 weeks time Please address any queries to worm <at> sanger.ac.uk New Data: --------- - New Briggsae protein set brigpep2 - C.elegans BlastP/X results against brigpep2 - C.briggsae BLASTP against C.elegans, human, fly, yeast, SWALL - Using latest BLAT binary and optimised BLAT BEST/OTHER output for C.elegans ESTs (and Marc Vidal OSTs) C.elegans mRNAs Other nematode ESTs Non-Wormbase GenBank/EMBL C. elegans CDS sequence submissions New Fixes: ---------- The optimization of BLAT dataset improves identifying scoring best BLAT results for OSTs, ESTs, mRNAs, etc. Known Problems: -------------- - Some SNP data and a few transcript objects were missing, and will be fixed in the next regular release. - Missing sequence features like SL2 and will be included in the next release Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------ - tRNA predictions will be updated using latest tRNASCAN-SE-1.23 for WS112. - Ongoing optimization for validating evidences supporting gene models. -===================================================================================- Quick installation guide for UNIX/Linux systems ----------------------------------------------- 1. Create a new directory to contain your copy of WormBase, e.g. /users/yourname/wormbase 2. Unpack and untar all of the database.*.tar.gz files into this directory. You will need approximately 2-3 Gb of disk space. 3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org). 4. Use the acedb 'xace' program to open your database, e.g. type 'xace /users/yourname/wormbase' at the command prompt. 5. See the acedb website for more information about acedb and using xace. ____________ END _____________
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During the last 11 years we have been successfully presenting our training seminars in the UK. We have now decided to let the rest of the world have a chance! Listed here are the 3 seminars that we will be presenting in various locations around the world between now and March 2004. For further info please send us your details and we will send our information pack by return. 1 - Selling for Engineers - One-day Seminar The Selling for Engineers seminar is a good introduction to effective sales principles for people who are new to selling, and also a useful refresher for 'old hands'. It applies to selling both technical products and intangible services. Many Sales Engineers have been learning the technical skills of their job for years but have had little formal training in selling. This course helps correct that imbalance. Typical job titles of delegates: Sales Engineer, Account Executive and Business Development Manager. 2 - Telephone Sales Prospecting for Engineers - One-day Workshop This event is a practical workshop teaching people in technical companies how to find new customers on the phone. It is applicable to business development for both tangible products and intangible services. The first session addresses whom to target, what to say and how to handle problems. The remainder of the day consists of live sales calls with coaching from Robert Seviour; the objective being to give delegates some positive experiences of prospecting, make sales appointments and maybe sell something! Please note that this telephone sales prospecting event is restricted to a maximum of six delegates to permit individual coaching. 3 - Closing Techniques Workshop - One day workshop What if the customer says: " " 'It's too expensive' " " 'We're happy with our present supplier' " " 'I want to think about it' Can you handle these common objections? By far the most efficient way to be more profitable is to turn more of the enquiries you receive into paid orders. For this, the ability to resolve objections is critical - either you close or you lose the sale. And if you answer 'How much discount will you give me?' with: 'I'll ask my boss', you waste profit, which could be yours with a better reply. In only a day I will teach you techniques which overcome these objections and more. You will be able to use them immediately to win profitable orders. There is no need to lose business to your competitors or give big discounts. If you have never had any formal sales training or need a refresher, don't continue to work at a disadvantage. All courses are from 9am until 5pm and cost £300 per person per day Reservations and information Please contact Sue on: Tel: +44(0)1481 720 294 Fax: +44(0)1481 720 317 If sales training is not an issue for your company please reply to this email with the word "DELETE" in the subject line. We will remove your details promptly.
This is an automatic announcement that WormBase (http://www.wormbase.org) has just been updated. New releases occur roughly every 2 weeks. The text of the AceDB release notes, which contains highlights of the new data is attached. You can download the full AceDB files from: ftp://ftp.sanger.ac.uk/pub/wormbase/current_release/ New release of WormBase WS111, Wormpep111 and Wormrna111 Fri Oct 3 16:15:28 BST 2003 WS111 was built by Keith Bradnam ====================================================================== This directory includes: i) database.WS111.*.tar.gz - compressed data for new release ii) models.wrm.WS111 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS111-WS110.dbcomp - log file reporting difference from last release v) wormpep111.tar.gz - full Wormpep distribution corresponding to WS111 vi) wormrna111.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS111.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) yk2orf.WS111.gz - Latest set of ORF connections to each Yuji Kohara EST clone ix) gene_interpolated_map_positions.WS111.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS111.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS111.gz - for each C. elegans WormPep protein, lists Best blastp match human, fly, yeast, C. briggsae, and SwissProt & Trembl proteins. xii) best_blastp_hits_brigprot.WS111.gz - for each C. briggsae protein, lists Best blastp match human, fly, yeast, C. elegans, and SwissProt & Trembl proteins. Release notes on the web: ------------------------- http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE Primary databases used in build WS111 ------------------------------------ brigdb : 2003-09-22 - updated camace : 2003-09-23 - updated citace : 2003-09-19 - updated cshace : 2003-09-11 - updated genace : 2003-09-23 - updated stlace : 2003-09-23 - updated Genome sequence composition: ---------------------------- WS111 WS110 change ---------------------------------------------- a 32367165 32367165 +0 c 17780236 17780236 +0 g 17757587 17757587 +0 t 32368413 32368413 +0 n 95 95 +0 - 0 0 +0 Total 100273496 100273496 +0 Wormpep data set: ---------------------------- There are 19938 CDS in autoace, 22193 when counting 2255 alternate splice forms. The 22193 sequences contain 9,683,562 base pairs in total. Modified entries 97 Deleted entries 18 New entries 43 Reappeared entries 0 Net change +25 Status of entries: Confidence level of prediction ------------------------------------------------- Confirmed 4609 (20.8%) Partially_confirmed 12079 (54.4%) Predicted 5505 (24.8%) Status of entries: Protein Accessions ------------------------------------- Swissprot accessions 2408 (10.9%) TrEMBL accessions 17866 (80.5%) TrEMBLnew accessions 1881 (8.5%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22155 (99.8%) Locus <-> Sequence connections (cgc-approved) --------------------------------------------- Entries with locus connection 4479 GeneModel correction progress WS110 -> WS111 ----------------------------------------- Confirmed introns not is a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 785 | -10 | St Louis | 464 | -168 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 30 | 0 | St Louis | 32 | 1 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ No synchronisation issues There are no gaps remaining in the genome sequence -------------------------------------------------- For more info mail worm <at> sanger.ac.uk -===================================================================================- New Data: --------- Worm proteins and DNA sequences have been BLAST searched against a new refined set of yeast proteins from SGD which is smaller than before (many spurious ORFs removed). Also new set of IPI human proteins have been BLAST searched against worm protein and DNA sequences. New Fixes: ---------- Problems with disappearing SNP data finally sorted out. Some tRNAs were incorrectly connected to their parent sequence, they have now been fixed. Known Problems: -------------- Some problems with BLATX homologies (C. elegans DNA vs other nematode ESTs), under investigation Some problems with badly mapped SNPs, work in progress to fix this Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------ We will store GenBank GI numbers and cross reference them to our sequence objects so that you can navigate between EMBL protein IDs and GenBank GI numbers. New updated set of tRNA predictions will be included in WS112, these have been generated with the latest version of tRNA-scanSE and will mean small changes to some of our existing predictions (mostly small changes to start or end coordinates). Planned changes to WormBase front page. We are currently discussing whether to add more items to the WormBase front page to better highlight new/interesting data in each new database release. E.g. 'click to see list of new CGC worm-related papers included in database since last build'. If you have ideas for what you would (or wouldn't!) like to see on our front page we would be interested in your opinions, please email us at wormbase-help <at> wormbase.org -===================================================================================- Quick installation guide for UNIX/Linux systems ----------------------------------------------- 1. Create a new directory to contain your copy of WormBase, e.g. /users/yourname/wormbase 2. Unpack and untar all of the database.*.tar.gz files into this directory. You will need approximately 2-3 Gb of disk space. 3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org). 4. Use the acedb 'xace' program to open your database, e.g. type 'xace /users/yourname/wormbase' at the command prompt. 5. See the acedb website for more information about acedb and using xace. ____________ END _____________
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