Here are some of the most frequently asked questions, if you have any
other questions concerning GenDB, please
us.
- How can I try out GenDB? Is there a demo version?
We have setup a demo project that you can access
without login/password information. Please
notice the system requirements.
- Is GenDB available?
The first stable release of GenDB (Version 1.0.5) has
been available since November 2001. All releases of
GenDB-1 were only available upon request after signing a
cooperation agreement. Since GenDB-2.2 we distribute the
system under the GNU GPL, you can download a copy from
our ftp server.
- Under what license is GenDB available?
The current version of GenDB is released under the GNU General Public License.
- What are the system requirements for GenDB?
GenDB has been developed on Solaris on Sparc
platforms by SUN
Microsystems.
In addition to Solaris the system has been installed
on the following platforms:
- i386 PCs running Suse Linux
- i386 PCs running
Linux RedHat
The GenDB system should work on any UNIX platform. See
here for a list of required
Software.
- How can I contribute to GenDB?
Since GenDB is being
developed as an open genome annotation system for non-commercial
purposes, interested researchers or developers should feel free to
contribute by contacting
us. We also maintain a list of contributed
GenDB scripts in the GenDB
Wiki where programmers can share useful Perl scripts
that were implemented using the GenDB
API.
- I am writing a Perl script. How can I retrieve the
gene name annotated for a given CDS?
You can find some sample code here in the GenDB Wiki that should definitely work.
The gene name is stored in the attribute 'name' of a
functional annotation which is usually created during
the automatic Metanor annotation or by manually
annotating a gene. A CDS region then stores a reference
to the latest annotation which is accessible via
my $annotation = $cds->latest_annotation_function;
Fetching the gene name is then straightforward:
my $geneName = $annotation->name if ref $annotation;
You can also get all annotations of a CDS via
my @annotations =
$master->Annnotation->Function->fetchallby_region($cds);
- What about feature requests?
Feature requests can be submitted using our Bugzilla bug tracking system. Please
select 'Enhancement: Request for new feature or
enhancement' from the 'Severity' options list.
- How do I report bugs?
Please use our Bugzilla bug reporting system.
- What additional software do I need on top of
the operating system?
Please see the following
questions.
- Do I need non open-source software to run
GenDB?
While we try to be completely open-source, we still do not want
to re-invent every wheel that is out there. There are a number of
tools that are not free to non-academics.
A list of the tools required and where to obtain them is
below.
-
glimmer: (can be
substituted, later versions will offer support for
alternative gene predictors)
-
TMHMM: prediction of
transmembrane helices in proteins(nice to have)
-
SignalP: presence and location of signal peptide
cleavage sites in amino acid sequences
- What additional open-source software do I
need to run GenDB?
- Perl -- The
Perl programming language.
A number of perl modules are required. Using the CPAN shell (from the
perl distribution), you can use the following bundle file to
(automatically) install all required perl modules,
including those mentioned below.
- MySQL --
The MySQL database management system.
Or in fact another
relational DBMS (we did tests with PostgreSQL). You may have to implement some
code to port O2DBI to your DBMS.
-
O2DBI - Persistent Objects with O2DBI
(only needed
for changes in the data model)
-
XVCG - graph visualization tool.
One
way of looking at pathways data.
- What additional bioinformatics software do I
need to run GenDB?
-
PFSCAN - motif scan in a protein sequence
-
GFF2PS - visualizing annotations of genomic sequences
-
Blast - Basic Local Alignment Search Tool
-
SAPS - Statistical Analysis of Protein Sequences
-
bioperl - open
source Perl tools for bioinformatics, genomics and life science
research. (Should be automatically installed by the CPAN shell,
see above to perl modules required.)
-
EMBOSS -- a package of high-quality FREE
Open Source software for sequence analysis
- What additional databases do I
need to run GenDB?
Some bioinformatics tools (e.g. blade) use sequence
or motif databases to find information on a given query
sequence.
The following databases have been sucessfully used with GenDB.
Please note: In most cases you do not need the complete
database, only a subset is usually required for searching.
We map information to and from the following pathway or function
databases:
-
KEGG -- a metabolic pathway database
-
GO --
a gene ontology database
