EMBnet News bulletin of 17 Dec 2004

Laurent Falquet Laurent.Falquet at isrec.unil.ch
Fri Dec 17 10:57:14 CET 2004

* EMBnet News bulletin of 17-Dec-2004 *

Dear Users,

Courses in 2005 (registration opened)

We will organise several courses in 2005:

1) Bern     Feb 21-25: Introduction to Bioinformatics
2) Lausanne Feb28-Mar04: Learning Unix and Perl for biomedical researchers
3) Lausanne Sep 29-30: RNA world in Bioinformatics
4) Basel    Oct 10-14: Advanced 3D modelling

1) Introduction to Bioinformatics (BE)
This is our famous course for beginners. We describe the basics of
bioinformatics (mostly sequence analysis) and we provide the participants
with exercises using tools and databases available on the web.
Registration opened until February 1st:
For more information please contact Dr. Lorenza Bordoli
lorenza.bordoli at isb-sib.ch

2) Learning Unix and Perl for biomedical researchers (LS)
Using the web interface for Bioinformatics research is very
convenient for small amounts of data (e.g. less than 20 sequences).
As soon as researchers want to analyse more sequences (from 20 up to
thousands sequences or megabytes of data), the task becomes tedious.
The course aims at providing the very basic knowledge of Unix
command-line and PERL scripting abilities to analyse large amounts of
data by automating recurring tasks or by grouping several tasks into
one command.
This course is organised for biomedical researchers and no particular
programming knowledge is required. Only basic Unix skills is recommanded.
At the end of the week, participants should know how to:
- Import/export data from/to Excel spreadsheets
- Automatically Blast a given list of sequences and extract relevant
- Retrieve sequences from a list of AC/ID and convert them to different formats
- Presentation and usage of some EMBOSS programs (e.g. Restriction
Mapping, ...)
- Creation of a basic web interface to your own programs
Registration opened until January 31:
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch

3) RNA world in Bioinformatics (LS)
This course aims to show important Bioinformatics tools related to
many forms of RNA (mRNA, tRNA, rRNA, gRNA, iRNA, mi/siRNA, telRNA).
These tools cover many aspects from detection, identification,
splicing, to folding predictions.
As this course complements the joint meeting of Villars/Ollon "Small
but powerfull" (Sept. 25-28, 2005), focus will be given to the
practicals with only a brief introduction. Only basic Unix skills is
Registration opened until June 30:
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch

4) Advance 3D modelling (BS)
This course is an extension of the introductory course to 3D modelling.
The detailed program and registrationn to be announced later here:
For more information please contact Dr. Lorenza Bordoli
lorenza.bordoli at isb-sib.ch

EMBL 81 is available

The EMBL Nucleotide Sequence Database was frozen to make Release 81 on
26-NOV-2004. The release contains 46,105,397 sequence entries
comprising 79,271,300,840 nucleotides,of which 5,408,558 entries
(34,986,041,399 nucleotides) are WGS (whole genome shotgun) data.

A breakdown of Release 81 by division is shown below:

Standard entries + CON entries

Division               Entries     Nucleotides
----------------- ------------ ---------------
Constructed            379,825  15,705,764,672
ESTs                24,481,418  12,837,493,911
Fungi                  110,405     221,397,562
GSSs                10,726,912   6,608,825,736
HTC                    327,042     407,601,536
HTG                     68,564  11,613,533,555
Human                  292,205   4,126,190,851
Invertebrates          175,545     677,544,114
Other Mammals           70,355     341,455,910
Mus musculus            96,306   2,330,916,828
Organelles             314,215     270,405,172
Patents              2,276,431   1,332,968,383
Bacteriophage            2,625      12,989,224
Plants                 287,510   1,084,488,061
Prokaryotes            282,227     993,811,176
Rodents                 31,538     110,601,526
STSs                   380,660     168,545,968
Synthetic               14,240      22,721,647
Unclassified             2,869       2,823,924
Viruses                262,346     241,496,438
Other Vertebrates      113,601     879,447,919
                   ------------ ---------------
Total               40,696,839  44,285,259,441

WGS entries
Division               Entries     Nucleotides
----------------- ------------ ---------------
Fungi                   21,561     423,823,856
Human                  601,855   8,075,925,526
Invertebrates          504,632   2,611,005,658
Other Mammals        2,851,288  15,053,696,865
Mus musculus           224,733   2,570,248,549
Plants                  88,097     817,835,696
Prokaryotes             14,549     306,011,654
Rodents                137,910   2,571,104,688
Unclassified           813,827     826,809,393
Viruses                     88         646,990
Other Vertebrates      150,018   1,728,932,524
                   ------------ ---------------
Total                5,408,558  34,986,041,399

EMBL database statistics are available at
URL: http://www3.ebi.ac.uk/Services/DBStats/

Note: The nucleotide count for CON(structed) entries is included
in the table, but not in the total. The nucleotide count for the
segments of a CON entry is included in the taxonomic divisions.

How to contact us ?

Don't forget our official help desk email address:

helpdesk at mail.ch.embnet.org

When sending an email to this address you will automatically receive
a ticket with a number. Your question will be answered by our team
or by an expert in the field from the Swiss Institute of Bioinformatics.

We wish you a Merry Christmas and Happy New Year.

Laurent Falquet, Swiss EMBnet node manager
and the Swiss EMBnet team members,
Lorenza Bordoli
Vassilios Ioannidis

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