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Search: Posts Made By: nekrut
Forum: Academic/Non-Profit Jobs 08-20-2013, 07:01 AM
Replies: 0
Views: 1,411
Posted By nekrut
Penn States seeks experienced systems engineer to build new biomedical computation in

The new initiative in Biomedical Computation at Penn State is seeking a highly experienced computational scientist to design, build, and maintain brand new infrastructure for supporting biomedical...
Forum: Bioinformatics 11-28-2010, 06:31 AM
Replies: 7
Views: 2,484
Posted By nekrut
Rafi: We just enabled an upload through an...

Rafi:

We just enabled an upload through an ftp. Take a look at the instructions at the upload interface. Let me know if you have issues.
Forum: Events / Conferences 05-24-2010, 12:58 PM
Replies: 0
Views: 1,420
Posted By nekrut
DAM-SIG 2010 | July 9 | Boston

DAM SIG 2010 ABSTRACTS

The abstract deadline for the DAM (Data and Analysis Management) SIG held in conjunction with ISMB 2010 in Boston has been EXTENDED to June 1st 2010 to allow for the...
Forum: Bioinformatics 05-18-2010, 06:14 AM
Replies: 5
Views: 7,773
Posted By nekrut
Galaxy's (http://usegalaxy.org) pileup parser...

Galaxy's (http://usegalaxy.org) pileup parser might do the trick:
http://bit.ly/cXtqD9
Forum: Bioinformatics 05-06-2010, 05:33 AM
Replies: 36
Views: 23,465
Posted By nekrut
Nils: Thanks for sending us your wrappers....

Nils:

Thanks for sending us your wrappers. They will be on public site shortly!
Forum: Bioinformatics 04-22-2010, 10:06 AM
Replies: 36
Views: 23,465
Posted By nekrut
Just talked to Bob Grossman. Will try...

Just talked to Bob Grossman. Will try...
Forum: Bioinformatics 04-14-2010, 11:42 AM
Replies: 36
Views: 23,465
Posted By nekrut
We have not see the data ourselves yet, but I...

We have not see the data ourselves yet, but I just asked Helicos guys to send us a few files. Do you have any to share?
Forum: Bioinformatics 04-09-2010, 05:16 AM
Replies: 36
Views: 23,465
Posted By nekrut
Yes, you can. The best way to get data in is to...

Yes, you can. The best way to get data in is to upload gzipped files via URL (http and ftp both work). See post #21 in the thread (scroll up).
Forum: Bioinformatics 04-01-2010, 05:57 AM
Replies: 36
Views: 23,465
Posted By nekrut
No limit as of now

No limit as of now
Forum: Bioinformatics 03-26-2010, 01:39 PM
Replies: 36
Views: 23,465
Posted By nekrut
Hi, upload limitations are going to be a problem...

Hi, upload limitations are going to be a problem for all of us as it is not Galaxy issue per se. To upload your files try this:
- gzip them
- put them to a web-accessible loocation
- paste a URL...
Forum: Bioinformatics 03-25-2010, 07:51 AM
Replies: 36
Views: 23,465
Posted By nekrut
New Quickies explaining fastq manipulation

Just added two movies explaining fastq manipulation: basic (http://screencast.g2.bx.psu.edu/galaxy/quickie_13_fastq_basic/flow.html) and advanced...
Forum: Bioinformatics 03-24-2010, 07:29 AM
Replies: 36
Views: 23,465
Posted By nekrut
Great. We'll give it a shot and make a wrapper in...

Great. We'll give it a shot and make a wrapper in a few weeks.
Forum: Bioinformatics 03-24-2010, 07:14 AM
Replies: 2
Views: 1,468
Posted By nekrut
Browsers do not usually like large uploads. The...

Browsers do not usually like large uploads. The alternative is to put your files into a web-accessible location feed Galaxy the URL through the Upload as shown in the attached image. Let us know if...
Forum: Bioinformatics 03-23-2010, 07:01 PM
Replies: 36
Views: 23,465
Posted By nekrut
We prefer to stay on the open source side of the...

We prefer to stay on the open source side of the world = how else do you know what software actually does?:rolleyes:
Forum: Bioinformatics 03-23-2010, 12:41 PM
Replies: 36
Views: 23,465
Posted By nekrut
Cufflinks by early summer. No plans for DegSeq...

Cufflinks by early summer. No plans for DegSeq yet (but integrating tools into Galaxy is easy, so anyone can do this). Speaking of Eland/Erange - we give priority to Open Source tools.
Forum: Bioinformatics 03-23-2010, 11:53 AM
Replies: 36
Views: 23,465
Posted By nekrut
At the time the challenge was the interpretation...

At the time the challenge was the interpretation of SAM output produced by BWA on solid reads. It will be quite simple to enable BWA for SOLiD in Galaxy, since all cs indices are alreay built. Do you...
Forum: Bioinformatics 03-23-2010, 11:47 AM
Replies: 36
Views: 23,465
Posted By nekrut
Dear Peter: Yes, this is on the to do list,...

Dear Peter:

Yes, this is on the to do list, and since we have 454s here this will be happening soon.
Forum: Bioinformatics 03-22-2010, 01:33 PM
Replies: 36
Views: 23,465
Posted By nekrut
Free & Open Environment for NGS analysis: Galaxy (http://usegalaxy.org)

The Galaxy team is announcing the launch of the first free public resource for NGS analysis at http://usegalaxy.org. This service is the beginning of our campaign to provide free web-based utilities...
Forum: SOLiD 02-18-2010, 07:31 AM
Replies: 34
Views: 28,551
Posted By nekrut
Converting solid to fastq in Galaxy

Galaxy has a new tool called solid2fastq that converts fragment and mate-pair runs into fastq files that can be mapped by bowtie. The tool takes care of the "orphaned" mates and makes sure that in...
Forum: Events / Conferences 01-19-2010, 07:02 AM
Replies: 0
Views: 2,423
Posted By nekrut
1st Galaxy Developer Conference | NGS Tool Integration & Data Management

May 15 - 17, 2010
Cold Spring Harbor Laboratory
(immediately following the Biology of Genomes)
http://www.galaxyproject.org/dev2010


The true value of high throughput sequencing methodologies...
Forum: Events / Conferences 05-07-2009, 09:41 AM
Replies: 0
Views: 2,453
Posted By nekrut
ISMB 2009 SIG on Data and Analysis Management

DATE: June 27, 2009
LOCALE: Stockholm, Sweden (ISMB)

This session will serve as an open forum for introduction of cutting edge applications that mold data sources and analysis tools into a...
Forum: Academic/Non-Profit Jobs 04-15-2009, 08:23 AM
Replies: 0
Views: 13,637
Posted By nekrut
Galaxy team is looking for engineers and postdocs

The Galaxy Team at Penn State and Emory (http://galaxyproject.org) is looking for ambitious individuals to fill multiple postdoctoral and software engineering positions. Galaxy is used by thousands...
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