50 Recent Changes in GeneNetwork Web retrieved at 01:43 (GMT)

We changed Alexandria.utmem.edu as our develope machine and we install working copies for development in different ports. There are littles of changes for the installing ...

We meet the bug Type Byte has already been registered when I install GeneNetwork branches on Alexandria.This bug is generated by the third party library Numarray ...

Numarray is being phased out and replaced by numpy. http://www.stsci.edu/resources/software hardware/numarray/numarray.html http://numpy.scipy.org/ LeiYan 11 Nov ...

A Python keyword. LeiYan 11 Nov 2009

GeneNetwork Installation Requirements Hardware Items Minimum Recommended CPU 1GHz, 1 core 2GHz, 2cores Memory 2G 8G Disk Capacity ...

CentOS is an Enterprise class Linux Distribution derived from sources freely provided to the public by a prominent North American Enterprise Linux vendor. CentOS conforms ...

Users can link back in time to previous versions of GeneNetwork using our GeneNetwork Time Machine. Select the date and this will take you back to the version of GeneNetwork ...

GeneNetwork Web This web contains documentation for the project at the http://www.uthsc.edu University of Tennessee Health Science Center System Architecture ...

http://www.python.org/ LeiYan 09 Oct 2009

http://www.apache.org/ LeiYan 09 Oct 2009

MySQL is the world's most popular open source database software, with over 100 million copies of its software downloaded or distributed throughout its history. With ...

http://www.genenetwork.org/ LeiYan 16 Jul 2009

The following are the servers and services currently in use on the Genenetwork racks in 211 Link. If unspecified, OS for each machine is CentOS 5. The machines are ...

Subversion Introduction is a version control system like CVS that we use to manage the GeneNetwork code. There are two different ways to use Subversion to access the ...

Statistics for nop GeneNetwork Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic ...

Step by step documentation to perform annotation upgrades into GeneNetwork 1. Download Blat from http://genome test.cse.ucsc.edu/~kent/exe/ To download click on the ...

Standard Operating Protocols (SOP) Requirements for all data set providers We encourage you to provide us a detailed INFO file sample along with your data set. This ...

June 2, 2009. The tape drive works. There are two places where you tell the drive what to do, its web interface and the terminal on the machine it's connected to. ...

Dell PowerVault MD1000 System http://www.dell.com/ LeiYan 31 Jul 2009

Updating the SNP database Jul 2009 Note: In the future, I suggest using liftOver instead of re BLATTing everything. The mm9 position was taken from Jackson Laboratories ...

This script takes the output of liftOver directly and creates MySQL update syntax out of it. Perfect for smaller numbers of updates; if you have a lot of rows to update ...

Updating Assemblies (This was written specifically for mm8 to mm9, but should be the same across all assemblies and species.) Since the last assembly update (mm6 ...

This script will take a 3 column input file from Geno (or whatever table) that you exported as: chromosome, megabase, identifier. It will then output it as chrChromosome ...

To set up a password less SSH Login: http://nosheep.net/story/password less ssh login/ ssh/sftp/scp from ender to bean without being prompted for a password: 1 ...

There are two kinds of Server (hardware) and OS (software): 32 bits and 64 bits. This is very important for system performance. LeiYan 16 Jul 2009

Setting up the ftp server is easy. We use vsftpd, available on YUM. Install it, do some minor configuration, and you're done (http://www.linuxhomenetworking.com/wiki ...

Setting up the TWiki is pretty straightforward. The TWiki as we use it does not write to a database; it writes to files. To reproduce this TWiki, you copy those files ...

I'm currently working on setting up a Gentoo mirror. Gentoo provides a more stripped down operating system than CentOS, giving us more control over what's running ...

A utility made by UC Santa Cruz that will take a location on one assembly and replace that with the corresponding location on a new assembly. It works pretty well ...

UPDATE See the Gentoo article for help on Gentoo mirrors. UPDATE I've written a script called bundle script which does most of this (maybe even all) for you. You ...

Doesn't work. KevAdler 31 Dec 2008

Update: None of this exists. I am going to create 3 scripts which will do daily, weekly, and monthly backup on various important data/code files in our servers. ...

Daniel report a bug: Interval mapping crashed on 1431643 at B when select chromosome 13 and genetic scale. It is invoked by the function drawProbeSetPosition of intervalPage ...

Development Strategies and Other Plans This page will eventually contain a summary of ideas, discussion, and plans for improving GeneNetwork and integrating GN more ...

Introduction The Correlation dataset was introduced to GeneNetwork on 3/04/05. The dataset was generated using LSI. PubMed abstracts are collected for each gene ...

Web2QTL 132.192.47.10 / 192.168.1.201 (see diagram for a live status report of hardware configuration) Functional Summary: This is the development site computer ...

Dear Munish, (Grant) Could you please add a page or two to the GN TWiki site. I am trying to get our international collaborations documented. Please link to this site ...

Headmaster 132.191.63.196 / 192.168.1.128 Functional Summary: This machine is the LDAP server for the cluster. See LdapServer for more details on the LDAP ...

11 Jan 2007: BXD is done. Next will be LXS. 22 Jan 2007: LXS is done. BXD was re ordered. 26 Jan 2007: Tried different approaches: 1) load sts mouse position ...

GeneNetwork Codebase The GeneNetwork codebase is written in Python. It is available on /node apps/www/html/webqtl from WebqtlMachine or machines that mount it. In ...

Assorted Administration Notes Linux Virtual Server Tutorial http://www.ultramonkey.org/papers/lvs tutorial/html/ LVS NAT LVS Direct Routing Configure LVS: On Linux ...

To open the access for IPs or domains, edit /etc/hosts.allow. To add ssh accesses, add a line: example: sshd: ucsd.edu Then restart the service: service xinetd restart ...

132.192.47.24 Server of mapmanager.org Manage 7 node Mac cluster Open Directory Master LDAP server Place for QTLReaper to run ZhaohuiSun 18 ...

Same as Chr Length but the SpeciesId 1 (mouse) data is for mm8 instead of mm6. EvanW 17 Aug 2006

Same as the others, except I think this should be rn3 and not rn33. I have no idea what the data in GeneList rn3 is from; the Rat data has 13619 rows in both GeneList ...

A deprecated version of the Geno2 table. Still referenced in the active code, but should be switched whenever possible. EvanW 17 Aug 2006

Much like the Geno2 mySQL table. However, some of its columns should be moved to the ProbeSetPos table (see that entry for more information). This table stores the ...

Contains the same information as GeneList, but all the position data (including exonStarts/Exon Ends/cdsStart/cdsEnd) for species 1 is in mm8 as opposed to the mm6 ...

Web Server Setup (Beta server) Note: This section only applies to WebqtlMachine, which is currently the web server for our beta site http://webqtl.utmem.edu. This ...

Chr Length is a simple mySQL table that stores the length in base pairs of each chromosome for each species. Unfortunately, it does not store the length for each ...