User: Scott Cain

gravatar for Scott Cain
Scott Cain750
Reputation:
750
Status:
New User
Location:
Website:
http://gmod.org/
Last seen:
8 years, 2 months ago
Joined:
9 years, 4 months ago
Email:
1***@biostars.org

Posts by Scott Cain

<prev • 37 results • page 1 of 4 • next >
3
votes
1
answer
1.9k
views
1
answers
Answer: A: Gbrowse 2 For Arabidopsis
... Hi Daniel, Of course the reasonable place to ask this question is the GBrowse mailing list: https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse since it is likely that the owners of GBrowse2 instances for Arabidopsis are subscribed to that list. As it happens, I know of one such instance at P ...
written 8.2 years ago by Scott Cain750
1
vote
3
answers
1.7k
views
3
answers
Answer: A: Gbrowse2 & Mod_Fcgid
... Hello Gregor, I don't know off the top of my head, but the GBrowse mailing list is probably a better place to ask this question, as I know there are people on that list that run GBrowse under fastCGI: https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse When you write the list, please be sure t ...
written 8.3 years ago by Scott Cain750 • updated 9 months ago by RamRS27k
4
votes
2
answers
2.9k
views
2
answers
Answer: A: How To Link To Gbrowse And Load Custom Track From External Data
... The rice and maize browsers are different versions of GBrowse (1 and 2 respectively), but they both support the eurl cgi parameter. For example, this url works for MaizeGDB: http://gbrowse.maizegdb.org/gb2/gbrowse/maize_v2/?start=376000;stop=475999;ref=Chr1;width=800;eurl=http://5585rosemontway.com ...
written 8.4 years ago by Scott Cain750
0
votes
0
answers
7.2k
views
0
answers
Comment: C: Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
... I am not familiar with IGV, but the GFF3 doesn't make much sense. Is there a reference sequence named "test" defined somewhere? The only reference sequence in your snippet is (presumably) for chromosome 14, so I would expect "14" to be in the first column. ...
written 8.4 years ago by Scott Cain750
8
votes
7
answers
7.0k
views
7
answers
Answer: A: What Is Your Experience With Gmod Tools Or Alternatives?
... Hi Michael, While I obviously have a biased opinion, I thought I'd at least share some information on what can be done with GMOD tools. I'll take your bullet points and give some explanation or guidance on each: ontologies (anatomy, developmental stage, etc.) -- Chado is based on the use of onto ...
written 8.4 years ago by Scott Cain750
0
votes
7
answers
7.0k
views
7
answers
Comment: C: What Is Your Experience With Gmod Tools Or Alternatives?
... I don't think I'd put it that way exactly, qdjm. JBrowse is definitely the future of GMOD genome browsers, but it is no where near as feature complete as GBrowse yet. Generally, I suggest that people install both, as you will generally need GBrowse for the functionality it provides, and once you h ...
written 8.4 years ago by Scott Cain750
0
votes
2
answers
1.7k
views
2
answers
Comment: C: What Are, If Any, The Conventions For Encoding Extra Information In The Gff3 Nin
... Yes, but I meant, why do you want to do that? Who is it for, and what will they be using the GFF file for? ...
written 8.4 years ago by Scott Cain750
5
votes
8
answers
4.4k
views
8
answers
Comment: C: C And Fortran Programming Language
... I agree with everyone else here that C is the way to go (and with the commenter above about what C courses are likely to be like at your school), but disagree with FORTRAN being dead. It is still very much used by engineers. ...
written 8.4 years ago by Scott Cain750
0
votes
2
answers
1.7k
views
2
answers
Comment: C: What Are, If Any, The Conventions For Encoding Extra Information In The Gff3 Nin
... You mean that have protein information? Not that I can recall, though I can tell you that the GFF3 at NCBI has EC_number tags that violate the GFF3 spec (at least, they did the last time I checked). What is the end use that you have in mind? ...
written 8.4 years ago by Scott Cain750
3
votes
2
answers
1.7k
views
2
answers
Answer: A: What Are, If Any, The Conventions For Encoding Extra Information In The Gff3 Nin
... There are no conventions outside of the GFF3 spec, though I would note that the reserved tag "Note" has historically been used for descriptions in GBrowse, so if you're going to be using GBrowse, it makes sense to put descriptions there. Generally I suggest that you encode the information in such a ...
written 8.4 years ago by Scott Cain750

Latest awards to Scott Cain

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1451 users visited in the last hour