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Recent Activity
All posts created by lhughes
| Link to this post | posted 11 Jan, 2017 01:39 | |
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Phamerator.org You will need to set up an account (using a .edu address). If I've misssed any details, I'm sure Steve or Vic will fill you in. Lee |
Posted in: Web Phamerator → Are we there yet?
| Link to this post | posted 10 Jan, 2017 04:17 | |
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Thanks, Chris. I think we'll be fine with the Beta version for now. Lee |
Posted in: Starterator → Starterator version 1.1 released
| Link to this post | posted 08 Jan, 2017 02:27 | |
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Hi Chris, When I tried running a couple of phage on the v.1.1 version, I got an crash error after just a few phams (8 on one and 5 on the other). Both the phage I tried were BD1 phages (BeardedLady and Oliynyk). I switched back to the v.1.1.1Beta and everything seems to run fine. Thoughts? Lee |
Posted in: Starterator → Starterator version 1.1 released
| Link to this post | posted 23 Dec, 2016 00:31 | |
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Quick question about PhamDB databases. I have successfully installed it on my machine now (rather than using Dan's web-access version). However, all the phages show up as "singleton" in my database. I am presuming that the Genbank files don't include cluster information, so that is why there is no cluster information. Anyone know how I could edit the GB files so that they include the appropriate cluster information when I load them into PhamDB to generate a Phamerator database? Thanks, Lee |
Posted in: Phamerator → PhamDB: Make your own Phamerator databases
| Link to this post | posted 05 Aug, 2016 00:20 | |
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Chris: Just tried it on my machine as well. It stayed on version 1.1.0 and I definitely had internet connectivity in the Virtual Box. Even opened, closed and then reopened Starterator Beta to see if there was any change. Lee |
Posted in: Starterator → Beta Version 1.1.1 released
| Link to this post | posted 30 Jul, 2016 17:54 | |
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Ok - tried Sprinklers again in Beta after clearing Intermediate files. It worked then. Sorry I didn't try that the first time. Lee |
Posted in: Starterator → phage that crash starterator
| Link to this post | posted 28 Jul, 2016 20:48 | |
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Chris: I am running the Beta version of Starterator on a phage that I am doing QC on and it is failing. The phage is Sprinklers (C1) and it fails on Pham 192 of 232. Thanks, Lee |
Posted in: Starterator → phage that crash starterator
| Link to this post | posted 27 Jul, 2016 01:20 | |
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I like the gray scale/red font options. That comes across very easy to see. As Welkin mentioned, when there are too many starts (or too many tracks) it gets really hard to see anything. The font size example doesn't work as well (to me) as the 1st option did. Thanks for working on this! Lee |
Posted in: Starterator → Starterator UI updates
| Link to this post | posted 24 May, 2016 16:50 | |
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I will always remember David's infectious smile and the sincere joy and excitement he brought to our discussions of science and learning. He will be sorely missed. My thoughts go out to his colleagues, friends, and family. |
Posted in: Messages for Cabrini College → Messages for Cabrini College
| Link to this post | posted 27 Apr, 2016 16:03 | |
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Yes - that is it. It is really good for making small custom databases (I've used it to look at just Streptomyces genomes). I don't think you'd want to use it for a full database though because that would take quite a long time and use a lot of computing resources. Lee |
Posted in: Phamerator → Custom Database - HELP?