SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 26 Apr, 2018 13:55
DanRussell	Hi Andrea, As Debbie said, the "master" copy of Phamerator gets updated about once a week. PhagesDB checks every night to see if a new version exists and if so, installs it. Online Phamerator does the same, but might not check every night, which is why things may appear out-of-sync for a day or two. But thanks for letting us know, and I'll double-check that everything is working as intended. –Dan

Link to this post | posted 26 Apr, 2018 13:55

Hi Andrea,

As Debbie said, the "master" copy of Phamerator gets updated about once a week. PhagesDB checks every night to see if a new version exists and if so, installs it. Online Phamerator does the same, but might not check every night, which is why things may appear out-of-sync for a day or two. But thanks for letting us know, and I'll double-check that everything is working as intended.

–Dan

Posted in: Web Phamerator → Pham Number Discrepancy

Link to this post \| posted 27 Feb, 2018 16:55
DanRussell	FROM AN NIH LIST Dear All, An ORISE fellow position is available in my laboratory for a project involving virology and bioinformatics knowledge including computer language. This position provides a training opportunity for enthusiasts interested in developing bioinformatics tools and databases for virus detection, annotation, and characterization. The overall goal of the project is cell line and vaccine safety. Individuals that meet the requirements should submit their CV and contact information for three references. Thank you. Regards, Arifa Khan Supervisory Microbiologist Laboratory of Retrovirus Research Division of Viral Products Office of Vaccines Research and Review Center for Biologics Evaluation and Research U.S. Food and Drug Administration 10903 New Hampshire Ave Bldg. 52-72, Room 1216 Silver Spring, MD 20993 Tel no. 240-402-9631 Email: arifa.khan@fda.hhs.gov

Link to this post | posted 27 Feb, 2018 16:55

DanRussell

FROM AN NIH LIST

Dear All,

An ORISE fellow position is available in my laboratory for a project involving virology and bioinformatics knowledge including computer language. This position provides a training opportunity for enthusiasts interested in developing bioinformatics tools and databases for virus detection, annotation, and characterization. The overall goal of the project is cell line and vaccine safety.

Individuals that meet the requirements should submit their CV and contact information for three references.

Thank you.

Regards,
Arifa Khan
Supervisory Microbiologist
Laboratory of Retrovirus Research
Division of Viral Products
Office of Vaccines Research and Review
Center for Biologics Evaluation and Research
U.S. Food and Drug Administration
10903 New Hampshire Ave
Bldg. 52-72, Room 1216
Silver Spring, MD 20993
Tel no. 240-402-9631
Email: arifa.khan@fda.hhs.gov

Posted in: General Message Board → ORISE Fellow Position at FDA

Link to this post \| posted 26 Jan, 2018 20:48
DanRussell	GregFrederick@letu.edu We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail. We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis. I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you. Thoughts? Is it a server problem, something with our genome annotation or something else? Thanks. greg Hi Greg, To be clear: your problem is with BLAST, not auto annotation itself? Meaning you get all the features, but only some of them have BLAST results? BLASTing all genes can sometimes end up with genes being skipped, especially if done during peak hours. What phage are you working on? –Dan

Link to this post | posted 26 Jan, 2018 20:48

DanRussell

GregFrederick@letu.edu
We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail.

We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis.

I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you.

Thoughts? Is it a server problem, something with our genome annotation or something else?

Thanks. greg

Hi Greg,

To be clear: your problem is with BLAST, not auto annotation itself? Meaning you get all the features, but only some of them have BLAST results?

BLASTing all genes can sometimes end up with genes being skipped, especially if done during peak hours. What phage are you working on?

–Dan

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

Link to this post \| posted 26 Jan, 2018 20:46
DanRussell	ptsourkas Still not working for me, as of January 24 2018. I get "Glimmer failure" and "Annotation failure". Thanks, Philippos Hi Philippos, Is your DNA Master up to date? If you run Update does all look good? Any other weird errors popping up? I think the servers are working. You've entered the proper access code in the linked document? –Dan

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

Link to this post \| posted 22 Jan, 2018 20:04
DanRussell	Steven Caruso Those of us who use any of the alternate hosts still have to use the VM, sadly. Steve For now! I know the other Steve C. is working on having multiple databases available online, so at some point that will no longer be the case. –Dan

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

Link to this post \| posted 22 Jan, 2018 19:59
DanRussell	Randall DeJong Dan Russell, I am having a real issue with getting 2017 SEA VM working on our Windows 10 computers. Can you get me the 2016 SEA VM that is 32 bit? Cal Keen ckeen@calvin.edu Hi Cal, Did you see my email response? In short: we're not recommending that you install the Virtual Machine at all this year, unless you have a specific need for it. Do you want to proceed with installing anyway? –Dan

Link to this post | posted 22 Jan, 2018 19:59

DanRussell

Randall DeJong
Dan Russell,
I am having a real issue with getting 2017 SEA VM working on our Windows 10 computers. Can you get me the 2016 SEA VM that is 32 bit?

Cal Keen
ckeen@calvin.edu

Hi Cal,

Did you see my email response? In short: we're not recommending that you install the Virtual Machine at all this year, unless you have a specific need for it. Do you want to proceed with installing anyway?

–Dan

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

Link to this post \| posted 17 Jan, 2018 17:58
DanRussell	Hi Claire, I just added a "Last modified" date to the Google Sheet. It should auto-update anytime the list is changed and saved. The date itself is in cell B1. Hope that helps! –Dan

Posted in: Request a new function on the SEA-PHAGES official list → Approved list

Link to this post \| posted 17 Jan, 2018 17:56
DanRussell	I think perhaps our servers were just down around Jan 12. Is it working now? –Dan

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

Link to this post \| posted 03 Jan, 2018 16:30
DanRussell	noverby Dan, Hope your holidays have been going well! Just checking in on the status of the 2018 VM? I'd like to work on getting our updated task sequence prepared and ready to install over our J-Term. If the download links are available, that would be much appreciated! Thank you for all that you do! Nate Hi Nate, There will be no new VM for this academic year. Partly because Phamerator and Starterator reports are now available on the web, we decided that the VM would be optional for schools this year. If they want to, they can use the 2017 VM, but most functions should be available via the web now. –Dan

Link to this post | posted 03 Jan, 2018 16:30

DanRussell

noverby
Dan,

Hope your holidays have been going well!

Just checking in on the status of the 2018 VM? I'd like to work on getting our updated task sequence prepared and ready to install over our J-Term. If the download links are available, that would be much appreciated!

Thank you for all that you do!

Nate

Hi Nate,

There will be no new VM for this academic year. Partly because Phamerator and Starterator reports are now available on the web, we decided that the VM would be optional for schools this year. If they want to, they can use the 2017 VM, but most functions should be available via the web now.

–Dan

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

Link to this post \| posted 18 Dec, 2017 16:35
DanRussell	Hi Sarah, From BLASTing Phergie on PhagesDB, it looks like the break is caused by the insertion of a single C. In those other closely-related genomes, there are 4 Cs, but in Phergie there are 5. I went and found the assembly for Phergie, and in that region you can see that there are plenty of high-quality reads that all have 5 Cs isntead of 4. So it's not a sequencing error! Looks like a real mutation that broke that gene into two. –Dan

Link to this post | posted 18 Dec, 2017 16:35

DanRussell

Hi Sarah,

From BLASTing Phergie on PhagesDB, it looks like the break is caused by the insertion of a single C. In those other closely-related genomes, there are 4 Cs, but in Phergie there are 5.

I went and found the assembly for Phergie, and in that region you can see that there are plenty of high-quality reads that all have 5 Cs isntead of 4.

So it's not a sequencing error! Looks like a real mutation that broke that gene into two.

–Dan

Posted in: Gene or not a Gene → Lysin A split in 2 or sequencing error-B1 cluster

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