EMBnet News bulletin of 5 Jan 2006

Laurent Falquet Laurent.Falquet at isrec.unil.ch
Thu Jan 5 09:38:15 CET 2006


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* EMBnet News bulletin of 05-Jan-2006 *
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Dear Users,

Courses in 2006
---------------

We will organise several courses in 2006:

1) Geneva Feb 28-Mar03: Introduction to Bioinformatics
2) Basel  Mar 20-24: Biostatistics
3) Lausanne Sep 04-08: DNA Microarrays data analysis
4) Basel  Oct 09-13: Learning Unix and Perl for biomedical researchers


1) Introduction to Bioinformatics (GE)
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 January 31st:
http://www.3eme-cycle.ch/biologie/pages/registration_generic.html
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch

2) Biostatistics (BS)
This advanced course will touch a large panel of biological problems requiring
statistical data analysis, i.e. not only Microarrays!
Knowledge of statistics (or R package) would be an asset to fully
benefit from this course.
Registration will be announced soon on 
http://www.ch.embnet.ogr/pages/courses.html
or contact course organiser Dr. Lorenza.Bordoli at isb-sib.ch
This course is organized with the support of the Swiss Committee for  
Molecular Biology (SKMB) (http://www.usgeb.ch/skmb.html).

3) DNA Microarrays data analysis (LS)
The aim of this course is to familiarize graduate students with the 
DNA microarray technology and will focus on the analysis of gene 
expression data using computational tools. Basic knowledge of 
statistics (or R package) would be an asset to fully
benefit from this course. (In collaboration with Dr. Mauro Delorenzi 
and his group).
Registration opened until July 31st:
http://www.3eme-cycle.ch/biologie/pages/registration_generic.html
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch

4) Learning Unix and Perl for biomedical researchers (BS)
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
information
- 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 will be announced on http://www.ch.embnet.ogr/pages/courses.html
or contact course organiser Dr. Lorenza.Bordoli at isb-sib.ch
This course is organized with the support of the Swiss Committee for  
Molecular Biology (SKMB) (http://www.usgeb.ch/skmb.html).



EMBL release 85 is available
----------------------------

The EMBL Nucleotide Sequence Database was frozen to make Release 85 
on 30-NOV-2005. The release contains 64,739,883 sequence entries 
comprising 116,106,677,726 nucleotides,of which 12,088,383 entries 
(59,629,958,692 nucleotides) are WGS (whole genome shotgun) data.

The release 85 files total 58 GB compressed.

A breakdown of Release 85 by division is shown below:

Standard entries + CON entries
Division                     Entries     Nucleotides
--------------------------- ------------ ---------------
Constructed                      309,204  34,556,088,519
Environmental Samples            198,926     156,526,578
ESTs                          31,990,232  17,588,999,697
Fungi                            135,310     269,984,302
GSSs                          13,405,392   8,411,563,400
HTC                              427,374     526,114,986
HTG                               78,979  12,957,132,445
Human                            335,728   4,221,385,762
Invertebrates                    325,192     820,390,029
Other Mammals                    125,136     485,491,074
Mus musculus                     111,297   3,644,614,489
Patents                        2,993,949   1,793,959,854
Bacteriophage                      2,756      17,194,636
Plants                           442,344   1,688,043,125
Prokaryotes                      226,827   1,250,657,072
Rodents                           48,553     130,164,037
STSs                             879,628     494,742,256
Synthetic                         23,176      32,549,709
Third Party Annotation             4,737     331,786,916
Unclassified                         841       1,822,843
Viruses                          324,493     304,109,679
Other Vertebrates                261,426   1,349,486,145
                             ------------ ---------------
Total                         52,651,500  56,476,719,034
EMBL WGS Sub-divisions
Division                     Entries     Nucleotides
--------------------------- ------------ ---------------
Environmental Samples          1,037,484   1,061,221,997
Fungi                             45,376     985,241,808
Human                            782,751   8,576,597,201
Invertebrates                  1,083,149   6,045,735,414
Other Mammals                  6,283,291  25,925,154,384
Mus musculus                   1,062,676   5,480,746,797
Plants                            88,097     817,835,696
Prokaryotes                       28,874     718,640,699
Rodents                        1,414,449   7,328,429,912
Other Vertebrates                262,236   2,690,354,784
                             ------------ ---------------
Total                         12,088,383  59,629,958,692

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 a Happy New Year.

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




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