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All posts created by kbutela

| posted 13 Jan, 2022 18:08
When students finish annotation their genomes, we use this spreadsheet to track their changes. They document which genes were changed and rationale for functions. We then have students peer review each other's original annotation spreadsheets and document their reviews in this spreadsheet. I could see modifying this review document as a summary of your notes for the genome you annotated.
Posted in: Notes and Final FilesNotes format when using DNA Master
| posted 13 Jan, 2022 18:04
We use this attached spreadsheet for students to document their notes and conclusions during the annotation process.
Posted in: Notes and Final FilesNotes format when using DNA Master
| posted 11 Oct, 2021 17:27
Hi all-

We've successfully made it through direct isolation and purification this semester, but has anyone else noticed a consistently low isolation rate for Gordonia phages over the last two months? We usually have a very high success rate (50-70%) on direct isolation here in Pittsburgh, but it's dropped down to 20% this semester across all 10 of our sections. Has anyone else noticed issues with low isolation rates for Gordonia? I'm curious as to what could be happening.
Posted in: Phage Discovery/IsolationLow isolation rate for Gordonia terrae this semester
| posted 30 Aug, 2021 22:18
It sounds like you are having the same FTP connection issues within DNA Master that we encountered over the summer (see https://seaphages.org/forums/topic/5155/?page=2). We were able to download DNA Master onto Windows 10, but we cannot get DNA Master to complete its update. When we try to update, we get a message that DNA Master is updating helper programs, and when this reaches 3%, we get the error message "FTP failure," and DNA Master isn't able to fully update itself. This results in limited functionality of the program. BLAST searches fail, but I'm not certain what else also fails since I haven't done extensive testing.

The problem isn't with downloading DNA Master, the problem lies with DNA Master not being able to connect to the FTP site to update itself. We have been unable to solve this issue on our own.
Posted in: DNA MasterDNA Master Issue
| posted 28 Jun, 2021 16:45
Thanks Christian! I have the file checker running on my Mac now and I was able to successfully run it with a test genome. I have attached the original instructions file with my edits and screenshots. I encountered a few more hiccups but I was able to solve them, so I put in my workarounds and triggered error messages in the document on the steps where the problems occurred.
Posted in: Notes and Final FilesNew File Checker for Mac
| posted 28 Jun, 2021 14:21
Hi Christian-

Thanks for this new set of instructions! Unfortunately I still get stuck fairly early in the process. When I update my bash_profile file with

nano ~/.bash_profile
export $PATH=’$PATH:/usr/local/mysql/bin’

I get this error message:
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin=$PATH:/usr/local/mysql/bin': not a valid identifier
I am unsure how to proceed. I can try to create a new bash_profile file but other than this I'm out of ideas.

UPDATE: I looked on some help forums and they suggested changing
export $PATH=’$PATH:/usr/local/mysql/bin’
to
export PATH=’$PATH:/usr/local/mysql/bin’

This seems to have solved the problem and I am proceeding with the install. I am going to edit a version of the instructions as I go.
Edited 28 Jun, 2021 14:36
Posted in: Notes and Final FilesNew File Checker for Mac
| posted 25 Jun, 2021 20:26
Does anyone have instructions for installing the new flat file checker on MacOS? I'm trying from the pdm_utils page but keep hitting a lot of roadblocks with things not working as described.
Posted in: Notes and Final FilesNew File Checker for Mac
| posted 24 Jun, 2021 20:14
Update-Dan is working on troubleshooting the issue with DNA Master on Windows 10 machines. For now, it appears that new installations are problematic but existing installations are able to successfully update and have full functionality. Depending on the nature of the problem, Jeffrey Lawrence may need to modify some settings in DNA Master. I will keep everyone updated on the status of this issue.
Posted in: DNA MasterDNA master server down?
| posted 21 Jun, 2021 17:31
If the phams in question aren't orphams, I think the best choice would be to wait a few days and try again to access the reports. Another option would be to have the students clear their browser cache and cookies regularly just in case their browsers are going to outdated links and are showing the error message instead of the regular Starterator report.

Here is a link to my video on an intro to Starterator and how to access reports both from PECAAN and from PhagesDB. Hope it helps!

Start Site Evaluation Tools: Starterator
Posted in: StarteratorPham not found in Starterator
| posted 21 Jun, 2021 17:07
Hi Kathleen! Are your students accessing Starterator reports via PECAAN or directly through PhagesDB? If they are using PECAAN, I have a video demonstrating how to solve this issue.

kcornely
Greetings, all,
I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports?
Thanks very much!
Kathleen
Posted in: StarteratorPham not found in Starterator