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synt
7/2/13
pygr and local data sets newbie help
Hi guys, I'm very new to pygr and to python but after reading through the specs I think pygr will
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pygr and local data sets newbie help
Hi guys, I'm very new to pygr and to python but after reading through the specs I think pygr will
7/2/13
Vishal Patel
, …
Paul Rigor
25
6/20/13
Issue with building NLMSA
Hi Chris, So I got in touch with the Pyrex developer and he re-posted version 0.9.8.6 (among other
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Issue with building NLMSA
Hi Chris, So I got in touch with the Pyrex developer and he re-posted version 0.9.8.6 (among other
6/20/13
Tommy Tang
5/4/13
biodb down
Hi, It looks like biodb is down again. could you please fix it? Thanks. dir(worldbase) ^CTraceback (
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biodb down
Hi, It looks like biodb is down again. could you please fix it? Thanks. dir(worldbase) ^CTraceback (
5/4/13
Tommy Tang
5/4/13
biodb down
Hi, it looks like the biodb is down again. dir(worldbase) ^CTraceback (most recent call last): File
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biodb down
Hi, it looks like the biodb is down again. dir(worldbase) ^CTraceback (most recent call last): File
5/4/13
Stu Blair
,
foobaron
2
3/27/12
biodb down? please help!
Thanks for letting us know. Namshin restarted it over the weekend. -- Chris
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biodb down? please help!
Thanks for letting us know. Namshin restarted it over the weekend. -- Chris
3/27/12
Jacob Biesinger
,
Namshin Kim
3
10/7/11
biodb down again?
Well they aren't from me-- I'm just using download=True to grab hg19... -- Jake Biesinger
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biodb down again?
Well they aren't from me-- I'm just using download=True to grab hg19... -- Jake Biesinger
10/7/11
Jacob Biesinger
, …
Namshin Kim
3
9/19/11
biodb down?
biodb2 pygr server has been restarted. Please check it again. On Tue, Sep 20, 2011 at 7:44 AM, Diane
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biodb down?
biodb2 pygr server has been restarted. Please check it again. On Tue, Sep 20, 2011 at 7:44 AM, Diane
9/19/11
Diane Trout
8/11/11
bsddb-free pygr
Hi, I fiddled some more with dbsqlite and figured out how to use github. I pushed a patch that
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bsddb-free pygr
Hi, I fiddled some more with dbsqlite and figured out how to use github. I pushed a patch that
8/11/11
Diane Trout
8/11/11
Poking at dbsqlite.py
Hello, I was trying to build an annotation file on an ubuntu 11.04 system and was getting unicode
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Poking at dbsqlite.py
Hello, I was trying to build an annotation file on an ubuntu 11.04 system and was getting unicode
8/11/11
Christopher Lee
6/23/11
fixed Ensembl interface problem
Hi, for those of you who may be trying to use the Ensembl interface included in Pygr 0.8.2, I just
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fixed Ensembl interface problem
Hi, for those of you who may be trying to use the Ensembl interface included in Pygr 0.8.2, I just
6/23/11
Brad Chapman
6/2/11
Early registration for BOSC ends tomorrow, Friday June 3
If you haven't already registered for BOSC, now is your chance--after June 3, prices will go up!
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Early registration for BOSC ends tomorrow, Friday June 3
If you haven't already registered for BOSC, now is your chance--after June 3, prices will go up!
6/2/11
Brad Chapman
4/12/11
Bioinformatics Open Source Conference (BOSC 2011)--Abstracts due April 18th!
Only one week left to submit an abstract to BOSC 2011! We have two great keynote speakers lined up (
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Bioinformatics Open Source Conference (BOSC 2011)--Abstracts due April 18th!
Only one week left to submit an abstract to BOSC 2011! We have two great keynote speakers lined up (
4/12/11
Christopher Lee
,
Diane Trout
2
3/24/11
Fwd: [pygr] biodb2.bioinformatics.ucla.edu
On Thu, Mar 24, 2011 at 10:25:38AM -0700, Christopher Lee wrote: > Hi Diane, > Namshin has
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Fwd: [pygr] biodb2.bioinformatics.ucla.edu
On Thu, Mar 24, 2011 at 10:25:38AM -0700, Christopher Lee wrote: > Hi Diane, > Namshin has
3/24/11
Diane Trout
3/23/11
biodb2.bioinformatics.ucla.edu
Hi, I noticed biodb2.bioinformatics.ucla.edu was down and making the default pygr worldbase cranky.
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biodb2.bioinformatics.ucla.edu
Hi, I noticed biodb2.bioinformatics.ucla.edu was down and making the default pygr worldbase cranky.
3/23/11
Brad Chapman
3/4/11
Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts
We invite you to submit an abstract to BOSC 2011! Please forward this message as appropriate, and
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Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts
We invite you to submit an abstract to BOSC 2011! Please forward this message as appropriate, and
3/4/11
Brad Chapman
2/24/11
BOSC 2011 topic organizers and Codefest
Hi all; This year the Bioinformatics Open Source Conference (BOSC) will be taking place in Vienna,
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BOSC 2011 topic organizers and Codefest
Hi all; This year the Bioinformatics Open Source Conference (BOSC) will be taking place in Vienna,
2/24/11
Naomi Ellen
, …
C. Titus Brown
12
12/24/10
[pygr] bsddb unavailable
Naomi, you might also consider using screed, which stores sequences in a sqlite database directly.
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[pygr] bsddb unavailable
Naomi, you might also consider using screed, which stores sequences in a sqlite database directly.
12/24/10
Christopher Lee
,
C. Titus Brown
2
12/24/10
testing dbsqlite in Pygr
On Thu, Dec 23, 2010 at 11:21:56AM -0800, Christopher Lee wrote: > the endless problems with dbm
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testing dbsqlite in Pygr
On Thu, Dec 23, 2010 at 11:21:56AM -0800, Christopher Lee wrote: > the endless problems with dbm
12/24/10
Scott
,
C. Titus Brown
2
12/11/10
Empty sequence intervals
On Fri, Dec 10, 2010 at 01:04:41PM -0800, Scott wrote: > Thanks for all the work on pygr, it's
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Empty sequence intervals
On Fri, Dec 10, 2010 at 01:04:41PM -0800, Scott wrote: > Thanks for all the work on pygr, it's
12/11/10
Steve Moss
11/16/10
PyGr Ensembl interface...
Hi, I noticed from the site, that the EnsEMBL interface is listed as only working with PyGr 0.7? What
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PyGr Ensembl interface...
Hi, I noticed from the site, that the EnsEMBL interface is listed as only working with PyGr 0.7? What
11/16/10
Kenny Daily
10/8/10
Issues with allowing empty NLMSA?
Are there any issues in allowing the creation of an empty NLMSA? I see in the cnestedlist code, it
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Issues with allowing empty NLMSA?
Are there any issues in allowing the creation of an empty NLMSA? I see in the cnestedlist code, it
10/8/10
Chris Fuller
,
Namshin Kim
3
10/4/10
Problems Building NLMSA from MAF
Hi Namshin, Thank you for the prompt reply on this. I eventually gave up trying to understand the
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Problems Building NLMSA from MAF
Hi Namshin, Thank you for the prompt reply on this. I eventually gave up trying to understand the
10/4/10
Taylor
,
Christopher Lee
2
8/27/10
pygr + sge
Not that I'm aware of. I used the coordinator module for running jobs over ssh a long time ago,
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pygr + sge
Not that I'm aware of. I used the coordinator module for running jobs over ssh a long time ago,
8/27/10
Julien Bellis
,
Christopher Lee
3
8/25/10
Fwd: Blast in pygr
Hi Chris, thanks for your answer. I tried with your settings but it doesn't help to make the
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Fwd: Blast in pygr
Hi Chris, thanks for your answer. I tried with your settings but it doesn't help to make the
8/25/10
Marek Szuba
2
8/18/10
Pygr and Python-2.7
On Fri, 23 Jul 2010, Marek Szuba wrote: > I'll set this branch up for llpygr megatests soon.
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Pygr and Python-2.7
On Fri, 23 Jul 2010, Marek Szuba wrote: > I'll set this branch up for llpygr megatests soon.
8/18/10
Marek Szuba
8/18/10
Pygr Windows binary packages on Win7
Hello guys, Could anyone (Titus? :-) see whether the Pygr binary packages for Windows we build, using
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Pygr Windows binary packages on Win7
Hello guys, Could anyone (Titus? :-) see whether the Pygr binary packages for Windows we build, using
8/18/10
jbiesinger
,
Christopher Lee
8
8/11/10
Pygr to print MSA from UCSC
Hi Jake, I have posted a fix for this to the "regions" branch of my github repository.
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Pygr to print MSA from UCSC
Hi Jake, I have posted a fix for this to the "regions" branch of my github repository.
8/11/10
Christopher Lee
8/7/10
problem running test file
Hi, I just ran into an annoying problem trying to run an individual test file. It seems we have
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problem running test file
Hi, I just ran into an annoying problem trying to run an individual test file. It seems we have
8/7/10
Jacob Biesinger
,
C. Titus Brown
2
7/23/10
Accessing AnnotDB's from NLMSA?
On Fri, Jul 23, 2010 at 11:30:23AM -0700, Jacob Biesinger wrote: > Is there a simple way to get
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Accessing AnnotDB's from NLMSA?
On Fri, Jul 23, 2010 at 11:30:23AM -0700, Jacob Biesinger wrote: > Is there a simple way to get
7/23/10
jbiesinger
, …
Namshin Kim
5
7/6/10
biodb2 down?
Hi, I just restarted biodb2 server. It seems it has been down for three days. I don't think it is
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biodb2 down?
Hi, I just restarted biodb2 server. It seems it has been down for three days. I don't think it is
7/6/10