SEA-PHAGES | All posts created by DanRussell

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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

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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