SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 16 Sep, 2015 18:19
DanRussell	Thanks to you both! Hopefully this will help anyone who's looking to avoid purchasing extra Windows licenses, or just prefers working on a Mac and doesn't want to bother with a Linux and a Windows VM. –Dan

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 16 Sep, 2015 13:55
DanRussell	Hi all, Does anyone have experience using Wine to run DNA Master on a Mac without having to install a Windows virtual machine? If so, any words of wisdom/caution/warning/enthusiasm? Thanks, –Dan

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 15 Sep, 2015 15:20
DanRussell	Yep, that looks like D29! Glad it's working.

Posted in: Phage Discovery/Isolation → Smeg grown in 7H9 Complete W/ or W/O Tween for enrichment???

Link to this post \| posted 14 Sep, 2015 19:07
DanRussell	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

Link to this post | posted 14 Sep, 2015 19:07

DanRussell

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

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

Link to this post \| posted 11 Sep, 2015 20:57
DanRussell	EDIT: The numbers have changed since I made a few small fixes and re-posted the VM files. The new numbers are: `MD5 (2016SEAVM_Mac.vmdk.zip) = 96e40fcce378c0d46855300f0aae61f5` `MD5 (2016SEAVM_PC.zip) = f457cbf5a82e2f66a5265eac6fe4979f` Hi Chris, I moved this to its own thread since it might be of interest to others. Here they are: ~~MD5 (2016SEAVM_Mac.vmdk.zip) = e6e6493548b1759e51ed0a6a516efc1c~~ ~~MD5 (2016SEAVM_PC.zip) = 7091845a11d28f9206a64d71b2c6ad35~~ –Dan Edited 16 Oct, 2015 20:14

Link to this post | posted 11 Sep, 2015 20:57

DanRussell

EDIT:

The numbers have changed since I made a few small fixes and re-posted the VM files. The new numbers are:

MD5 (2016SEAVM_Mac.vmdk.zip) = 96e40fcce378c0d46855300f0aae61f5

MD5 (2016SEAVM_PC.zip) = f457cbf5a82e2f66a5265eac6fe4979f

Hi Chris,

I moved this to its own thread since it might be of interest to others.

Here they are:
~~MD5 (2016SEAVM_Mac.vmdk.zip) = e6e6493548b1759e51ed0a6a516efc1c~~
~~MD5 (2016SEAVM_PC.zip) = 7091845a11d28f9206a64d71b2c6ad35~~

–Dan

Edited 16 Oct, 2015 20:14

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

Link to this post \| posted 02 Sep, 2015 21:09
DanRussell	sbconant Is there any way someone might be able to send me a pdf of "The secret lives of mycobacteriophages"?? I cant seem to access it through our or Wayne State's library system. Thanks! Hi Stephanie, As long as you're using it in line with the disclaimers on the first page, we should be fine sharing it with you (and others) directly. Here it is! –Dan

Posted in: Papers → Introductory Phage Papers

Link to this post \| posted 01 Sep, 2015 16:17
DanRussell	Hi Stephanie, I moved your question to the "Papers" forum since it seems more at home here. One source to check out is the PhagesDB "PubGroups". These are groups of publications that share some theme. The "Faculty Favorites" are papers that come with recommendations by SEA-PHAGES faculty members. This page on seaphages.org also has papers that have been authored in part by SEA-PHAGES undergrads or faculty. Finally, here are just a few direct suggestions that might be good for getting students' feet wet. The secret lives of mycobacteriophages. (Review article.) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches –Dan Edited 01 Sep, 2015 16:20

Link to this post | posted 01 Sep, 2015 16:17

DanRussell

Hi Stephanie,

I moved your question to the "Papers" forum since it seems more at home here.

One source to check out is the PhagesDB "PubGroups". These are groups of publications that share some theme. The "Faculty Favorites" are papers that come with recommendations by SEA-PHAGES faculty members.

This page on seaphages.org also has papers that have been authored in part by SEA-PHAGES undergrads or faculty.

Finally, here are just a few direct suggestions that might be good for getting students' feet wet.

The secret lives of mycobacteriophages. (Review article.)

Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage.

Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches

–Dan

Edited 01 Sep, 2015 16:20

Posted in: Papers → Introductory Phage Papers

Link to this post \| posted 26 Aug, 2015 20:05
DanRussell	Hi Sharon, Short answer: no. The upcoming version of the Virtual Machine (which will be called the 2016 SEA VM) will only differ from the 2015 SEA VM in the following ways: Ubuntu system software will be updated to ensure the latest security patches are incorporated. Consed will be updated to the latest version. The 2015 SEA VM only differed from the 2014 SEA VM in that it had Starterator installed by default. If you only plan on using Phamerator, and already have the 2014 or 2015 VM installed, you'll be fine. If you're starting from scratch, you might as well get the most updated version, the 2016 SEA VM. I'll post a link to it here when it's ready for download! –Dan

Link to this post | posted 26 Aug, 2015 20:05

DanRussell

Hi Sharon,

Short answer: no.

The upcoming version of the Virtual Machine (which will be called the 2016 SEA VM) will only differ from the 2015 SEA VM in the following ways:

Ubuntu system software will be updated to ensure the latest security patches are incorporated.
Consed will be updated to the latest version.

The 2015 SEA VM only differed from the 2014 SEA VM in that it had Starterator installed by default.

If you only plan on using Phamerator, and already have the 2014 or 2015 VM installed, you'll be fine. If you're starting from scratch, you might as well get the most updated version, the 2016 SEA VM. I'll post a link to it here when it's ready for download!

–Dan

Posted in: SEA-PHAGES Virtual Machine → Changes to Virtual Machine for 2015-16?

Link to this post \| posted 17 Aug, 2015 15:26
DanRussell	cdshaffer OK I thought it would be a good idea to have a thread with any solutions people have found for starterator crashing. I will start please feel free to add to the list. 1. Name of phage: I found that when I typed in phage name "Mana" it would crash but entering "Mana_draft" worked. The crashing in this case was due to some name confusion with Manad, probably because Mana is found entirely within Manad. 2. Some crashes have been fixed by deleting older files cached by starterator. These files can be found by going to your home directory, and select the menu item View -> "show hidden files" Once you select that, you will see many more files and folders in your home directory. Open the folder .starterator and inside there is a folder called "Intermediate Files". I have fixed many crashes by deleting all files in that folder and running starterator again. Hey Chris, Thanks for documenting these issues. Hopefully, others can use these solutions, or we can eventually rework Starterator itself to avoid them! –Dan

Link to this post | posted 17 Aug, 2015 15:26

DanRussell

cdshaffer
OK I thought it would be a good idea to have a thread with any solutions people have found for starterator crashing. I will start please feel free to add to the list.

1. Name of phage: I found that when I typed in phage name "Mana" it would crash but entering "Mana_draft" worked. The crashing in this case was due to some name confusion with Manad, probably because Mana is found entirely within Manad.

2. Some crashes have been fixed by deleting older files cached by starterator. These files can be found by going to your home directory, and select the menu item View -> "show hidden files"
Once you select that, you will see many more files and folders in your home directory. Open the folder .starterator and inside there is a folder called "Intermediate Files". I have fixed many crashes by deleting all files in that folder and running starterator again.

Hey Chris,

Thanks for documenting these issues. Hopefully, others can use these solutions, or we can eventually rework Starterator itself to avoid them!

–Dan

Posted in: Starterator → Read First: Common Starterator Troubleshooting

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