SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 08 Jan, 2016 20:18
DanRussell	klloyd-davies Hi Dan, I work at WSU's VetMed IT and have been asked to install the VM in one of our student labs per Bill Davis. He provided the software and I've got it up and running, but I need admin credentials to install the Guest Additions. Would you be able to email me the password for either the SEA Faculty or SEA Admin accounts? I assume Dr. Davis has them, but he's out today and I would like to finalize the setup before students are back on Monday. Thank you, Keith Lloyd-Davies Hi Keith, Just emailed them to you! –Dan

Link to this post | posted 08 Jan, 2016 20:18

klloyd-davies
Hi Dan,

I work at WSU's VetMed IT and have been asked to install the VM in one of our student labs per Bill Davis. He provided the software and I've got it up and running, but I need admin credentials to install the Guest Additions. Would you be able to email me the password for either the SEA Faculty or SEA Admin accounts? I assume Dr. Davis has them, but he's out today and I would like to finalize the setup before students are back on Monday.

Thank you,
Keith Lloyd-Davies

Hi Keith,

Just emailed them to you!

–Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 05 Jan, 2016 17:42
DanRussell	DoTS_UWRF Dan Russell Sharon Isern Can students get access to the VM 2016 via seaphages.org? Or do they have to be logged in as faculty? We're in class right now. Thanks!! Because of the software included, we couldn't post it totally publicly. And since there's no "registered student" accounts on PhagesDB, there's no way to give them access to the protected page. That said, I'll email you (and any other faculty who want it) the magic link! –Dan Dan, Would it be possible to share the link with me via email or message? I work in the IT department at UWRF with Karen Klyzek and the account we used previously (under Gary Knigge) is no longer active to download the SEALinux VM. We are working on rebuilding the image for the department laptops and need to download the file. Thank you in advance, Nate Overby Division of Technology Services UW-River Falls Just sent them to you, Nate. Good luck. –Dan

Link to this post | posted 05 Jan, 2016 17:42

DanRussell

DoTS_UWRF
Dan Russell
Sharon Isern
Can students get access to the VM 2016 via seaphages.org? Or do they have to be logged in as faculty? We're in class right now. Thanks!!

Because of the software included, we couldn't post it totally publicly. And since there's no "registered student" accounts on PhagesDB, there's no way to give them access to the protected page.

That said, I'll email you (and any other faculty who want it) the magic link!

–Dan
Dan,

Would it be possible to share the link with me via email or message? I work in the IT department at UWRF with Karen Klyzek and the account we used previously (under Gary Knigge) is no longer active to download the SEALinux VM. We are working on rebuilding the image for the department laptops and need to download the file.

Thank you in advance,
Nate Overby
Division of Technology Services
UW-River Falls

Just sent them to you, Nate. Good luck.

–Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 07 Dec, 2015 21:05
DanRussell	jparker Eureka! Exactly what I need. I have never seen that page. What menu is it under? I can't seem to be find a link for it on PhagesDB. Now that I know it exists, i'll bookmark it, but it would be good to know how to direct students to the page. Thanks! Jordan Hi Jordan, I think I removed the menu link about 6 months ago when the Phamerator database on PhagesDB was out-of-date. But now that it's re-synced, I've put it back in. Now there's a "Phams" item in the Phages dropdown menu. Thanks for the reminder! –Dan

Link to this post | posted 07 Dec, 2015 21:05

DanRussell

jparker
Eureka! Exactly what I need. I have never seen that page. What menu is it under? I can't seem to be find a link for it on PhagesDB. Now that I know it exists, i'll bookmark it, but it would be good to know how to direct students to the page.
Thanks!
Jordan

Hi Jordan,

I think I removed the menu link about 6 months ago when the Phamerator database on PhagesDB was out-of-date. But now that it's re-synced, I've put it back in. Now there's a "Phams" item in the Phages dropdown menu. Thanks for the reminder!

–Dan

Posted in: Phamerator → Phams

Link to this post \| posted 07 Dec, 2015 05:31
DanRussell	jparker Thanks Nick and cdshaffer! I only know enough coding language to frustrate myself, so I'll probably leave that to the experts. Is there a straightforward way to generate lists of pham members without opening the pham circle tool? This may be a more complicated question than can be easily answered here. I'm headed to the in silico workshop in two weeks, so I should be able to get more info there. Thanks for your help! Jordan Hi Jordan, Depending on exactly what you want, you may be able to do this on PhagesDB as well. The Pham page lets you select a Pham of interest and view its members: http://phagesdb.org/phams/ For example: http://phagesdb.org/phams/1728/ –Dan

Link to this post | posted 07 Dec, 2015 05:31

DanRussell

jparker
Thanks Nick and cdshaffer! I only know enough coding language to frustrate myself, so I'll probably leave that to the experts. Is there a straightforward way to generate lists of pham members without opening the pham circle tool? This may be a more complicated question than can be easily answered here. I'm headed to the in silico workshop in two weeks, so I should be able to get more info there.
Thanks for your help!
Jordan

Hi Jordan,

Depending on exactly what you want, you may be able to do this on PhagesDB as well. The Pham page lets you select a Pham of interest and view its members:

http://phagesdb.org/phams/

For example:

http://phagesdb.org/phams/1728/

–Dan

Posted in: Phamerator → Phams

Link to this post \| posted 16 Nov, 2015 21:07
DanRussell	Steven Caruso Hello, Is there a link we can provide to our OIT depts or do I need to give them my log-in information? Steve Hi Steve, Because of some of the software installed, I can't post the link publicly, but I'll happily send it to you and you can share with whomever you need. If logged in as a faculty member, you can also look at the source html for the http://seaphages.org/software/virtualmachine/ page and get it from there! –Dan

Link to this post | posted 16 Nov, 2015 21:07

DanRussell

Steven Caruso
Hello,

Is there a link we can provide to our OIT depts or do I need to give them my log-in information?

Steve

Hi Steve,

Because of some of the software installed, I can't post the link publicly, but I'll happily send it to you and you can share with whomever you need. If logged in as a faculty member, you can also look at the source html for the http://seaphages.org/software/virtualmachine/ page and get it from there!

–Dan

Posted in: SEA-PHAGES Virtual Machine → md5 sum for 2016 Virtual Machine download files

Link to this post \| posted 10 Nov, 2015 18:30
DanRussell	Yep, you got it Lee. I made the original video with an older version of consed. The new syntax should be: `addSolexaReads.perl -ace your_ace_file.ace -fastqfof reads_file.fof -fasta fasta_file.fof` –Dan Edited 10 Nov, 2015 18:31

Posted in: Consed → Adding Illumina reads

Link to this post \| posted 27 Oct, 2015 21:19
DanRussell	Lee Hughes I just wanted to express my happiness to see that a new episode of "Sounds of the Sea" was released. I really enjoy the discussions of phage biology that are in those each time. Lee We have a fan! Glad you're enjoying them. We're happy to take any suggestions about topic/format/people that would make them more appealing/interesting. –Dan

Posted in: Phage Biology → Sounds of the Sea

Link to this post \| posted 20 Oct, 2015 15:22
DanRussell	cdshaffer Dan, Is there anyway to make this post sticky so it stays on top of the list. Might be helpful to new faculty to read this post first and try solutions before posting a question. Could we even change the title to add something like READ THIS FIRST or START HERE. Chris Done and done. And just as an addendum, the currently posted versions of the 2016 SEA VM have the corrected default Starterator and Phamerator databases. If you download the new VMs now, each program should default to the Actino_Draft database. –Dan

Link to this post | posted 20 Oct, 2015 15:22

DanRussell

cdshaffer
Dan,
Is there anyway to make this post sticky so it stays on top of the list. Might be helpful to new faculty to read this post first and try solutions before posting a question. Could we even change the title to add something like READ THIS FIRST or START HERE.
Chris

Done and done. And just as an addendum, the currently posted versions of the 2016 SEA VM have the corrected default Starterator and Phamerator databases. If you download the new VMs now, each program should default to the Actino_Draft database.

–Dan

Posted in: Starterator → Read First: Common Starterator Troubleshooting

Link to this post \| posted 05 Oct, 2015 14:00
DanRussell	Hi Jordan, Apologies, we haven't done a great job of letting everyone know the updated Phamerator settings. We've combined all of the Actinobacteria phages into a single Phamerator database. It is now available by using the following settings in Phamerator (go to Edit–>Preferences in Phamerator to change these values). Take care to type exactly, because these are all case-sensitive and must be input exactly as shown. Server: http://phamerator.webfactional.com/databases_Hatfull Database: Actino_Draft After entering both of these values, click "Force Database Update". Wait while Phamerator updates, then it'll prompt you to restart. Do that. If you're prompted for a password at any point, it should be simply: "phage". –Dan Edited 05 Oct, 2015 14:00

Link to this post | posted 05 Oct, 2015 14:00

DanRussell

Hi Jordan,

Apologies, we haven't done a great job of letting everyone know the updated Phamerator settings. We've combined all of the Actinobacteria phages into a single Phamerator database. It is now available by using the following settings in Phamerator (go to Edit–>Preferences in Phamerator to change these values).

Take care to type exactly, because these are all case-sensitive and must be input exactly as shown.

Server:
http://phamerator.webfactional.com/databases_Hatfull

Database:
Actino_Draft

After entering both of these values, click "Force Database Update". Wait while Phamerator updates, then it'll prompt you to restart. Do that. If you're prompted for a password at any point, it should be simply: "phage".

–Dan

Edited 05 Oct, 2015 14:00

Posted in: Phamerator → Databases and Alternate hosts

Link to this post \| posted 28 Sep, 2015 14:26
DanRussell	asjahfed Hi Dan, Were you able to figure out what the problem may be with the download? Thanks, -Asjah F. Hi Asjah, I haven't been able to figure out any download-specific problems. We've tested the downloads at several different places and they seem to work. Are you using a hard-wired connection or a wireless connection? I'd recommend hard-wired if you can. It's actually Dropbox that's serving the files, so it should be reputable and reliable. You could also try a different browser if you continue having trouble, or a different internet connection in case there are file-size limits on the ISP you're using. –Dan Edited 28 Sep, 2015 14:26

Link to this post | posted 28 Sep, 2015 14:26

DanRussell

asjahfed
Hi Dan,

Were you able to figure out what the problem may be with the download?
Thanks,

-Asjah F.

Hi Asjah,

I haven't been able to figure out any download-specific problems. We've tested the downloads at several different places and they seem to work.

Are you using a hard-wired connection or a wireless connection? I'd recommend hard-wired if you can. It's actually Dropbox that's serving the files, so it should be reputable and reliable. You could also try a different browser if you continue having trouble, or a different internet connection in case there are file-size limits on the ISP you're using.

–Dan

Edited 28 Sep, 2015 14:26

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

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