SEA-PHAGES | All posts created by DanRussell

← previous
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
next →

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

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

Link to this post \| posted 24 Sep, 2015 19:49
DanRussell	For anyone else who's looking, Starterator is installed only on the seastudent account, so you'll have to log into that one. There should be an icon on the left bar for Starterator thereafter. –Dan

Posted in: Starterator → Starterator in 2016 VM

Link to this post \| posted 21 Sep, 2015 13:56
DanRussell	asjahfed Hi, I have a PC and I've been trying to download and unzip the Sea VM file but I keep getting an error saying that the zip file is invalid. Can someone please help me if they have encountered the same problem or knows how to fix this. Thanks, -Asjah F. Hi Asjah, What version of Windows are you using? First I would verify that the entire file downloaded. You can check the size (~4.7 Gb) but I'd also suggest verifying the md5sum value to be completely sure you have the intact file. You can use a program like HashCheck on Windows to figure out the md5sum of the file you downloaded. It should exactly match the md5sum posted here. If you're sure you downloaded the entire file, and the md5sum matches, please post here and let us know, and we'll get to the bottom of it. –Dan

Link to this post | posted 21 Sep, 2015 13:56

DanRussell

asjahfed
Hi, I have a PC and I've been trying to download and unzip the Sea VM file but I keep getting an error saying that the zip file is invalid.

Can someone please help me if they have encountered the same problem or knows how to fix this.

Thanks,

-Asjah F.

Hi Asjah,

What version of Windows are you using? First I would verify that the entire file downloaded. You can check the size (~4.7 Gb) but I'd also suggest verifying the md5sum value to be completely sure you have the intact file. You can use a program like HashCheck on Windows to figure out the md5sum of the file you downloaded. It should exactly match the md5sum posted here.

If you're sure you downloaded the entire file, and the md5sum matches, please post here and let us know, and we'll get to the bottom of it.

–Dan

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

Link to this post \| posted 18 Sep, 2015 18:48
DanRussell	Okay, the Virtual Machine page is now public, but the download links are disabled unless a faculty member is logged in. In addition, only the student password is visible to non-faculty. Hope that works, and let me know if there are any issues. –Dan

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

Link to this post \| posted 18 Sep, 2015 18:06
DanRussell	cdshaffer Dan, Can you create a page that students can get to that has all the instructions for installing the machine just like on the protected /software/virtualmachine/ page? I would like to be able to point students to all those well written instruction on how to go about installing virtual machines once I give them the virtual disk I want them to use. thanks That's a good point, Chris. I'll try to rework the page so that it's open to everyone but only has the download links for logged-in faculty. –Dan

Link to this post | posted 18 Sep, 2015 18:06

DanRussell

cdshaffer
Dan,

Can you create a page that students can get to that has all the instructions for installing the machine just like on the protected /software/virtualmachine/ page? I would like to be able to point students to all those well written instruction on how to go about installing virtual machines once I give them the virtual disk I want them to use.

thanks

That's a good point, Chris. I'll try to rework the page so that it's open to everyone but only has the download links for logged-in faculty.

–Dan

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

← previous
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
next →

Recent Activity

All posts created by DanRussell