On 4 Dec 2006, at 16:19, Zacher, Stacy wrote:
Hi Arek:
Please confirm if the Biomart v0.5 is compatible with MySQL v5.x vs.
MySQL 4.x.
Thanks
Stacy Zacher
Hi Stacy,
most of our testing was done against MySQL v 4. However
biomart-perl was also tested against v 5 and seemed to be working ok.
Is it causing you any problems?
a.
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Arek Kasprzyk
Sent: Wednesday, November 29, 2006 5:27 AM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]; BioMart
(E-mail);
[EMAIL PROTECTED]
Subject: [mart-dev] BioMart version 0.5 released
BioMart 0.5, a new version of the query-oriented data management system
has been released. The new release comes with a number of new features
and
improvements:
MartView
========
BioMart web code has been re-implemented in order to make it easier to
set up and run queries. Filters and attributes now come in collapsible
panels, considerably improving the scalability of the interface. The
handling of two dataset queries has been much improved. It is now
possible to combine attributes as well as filters in such queries which
makes it possible to fully annotate a local dataset with a remote one.
Customization of options including colour schemes, result file
handling,
logging options etc is much easier to manage in the new code. Finally
it
is now possible to use the webcode with apache 2 as well as apache 1.
MartBuilder
===========
The first version of a new tool for creating BioMart compatible schemas
from existing relational data sources has been included in this
release.
It makes the task of designing, creating and managing the schema
transformation straightforward. MartBuilder allows you to select the
central table of interest in a database and automatically design
datasets based around that central table. It follows the BioMart
transformation guidelines and naming conventions and will generate SQL
statements that you can execute to perform the actual transformation.
API
====
The Web service and Perl APIs have been considerably simplified in
terms
of user friendliness. The Perl API and Web service follow exactly the
same simple query building pattern used by MartView. In addition it is
now possible to find all the necessary attribute and filter internal
names for building a query with one click of the MartView XML button.
MartShell
=========
MartShell now comes with auto-completion and command line history on
linux, mac and windows.
All the code and documentation is freely available and can be
downloaded
from http://www.biomart.org and the new web interface is accessible at
http://www.biomart.org/biomart/martview
On behalf of the BioMart team,
Arek Kasprzyk
-----------------------------------------------------------------------
-
-------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
-----------------------------------------------------------------------
-
-------
------------------------------------------------------------------------
-------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
------------------------------------------------------------------------
-------
