Link to this post | posted 19 Jun, 2023 19:25

kbutela

Fellow Mac Users- Several years ago, Mac users within the SEA community used a program called WINE to (see https://seaphages.org/forums/topic/17/?page=1 for a history) run DNA Master on MacOS without the need for a Windows-based virtual machine. With the release of MacOS Catalina, the ability to use WINE ended (see https://seaphages.org/forums/topic/4976/). I have been using a paid version of WINE called CrossOver to successfully run DNA Master on MacOS Ventura, but I wanted to let everyone know that I have also been successful in getting a free version of WINE called Wineskin Winery to run DNA Master on MacOS Monterey. If there is interest in the SEA community to revisit WINE, please respond to this thread and we can get a collaboration going.

Link to this post | posted 12 Jun, 2023 12:21
kbutela	Hi Steve- I have a manual update workaround that is not pretty to set up but seems to be functional. I'll reach out via email to set up a time where we can Zoom to discuss. I don't quite have written instructions ready to distribute, but more people testing the strategy will help. Thanks!

Link to this post | posted 01 Jun, 2023 18:42
kbutela	Phamerator is currently down for me and my students as of Thursday 6/1 at 2:30 pm. We just upgraded internet security services, so it's entirely possible that the site is blocked on campus wifi. Is anyone else having trouble?

Link to this post | posted 16 Sep, 2022 21:04

kbutela

Notes on using Gordonia as a host from the September 16, 2022 faculty meeting: Tips and tricks: Phage isolation success rate can vary; excessive rain may be reducing rates but generally wet weather is helpful Excessively saturated samples typically do not yield phages Drainage areas tend to be high-yield areas Small plaques: decrease top agar concentration (maybe to 0.3%) and reduce amount of cells Small plaques may also indicate phages that grow better on another strain of Gordonia Hosts currently used for host range Gordonia terrae CAG3, G. rubripertincta, G. westfalica, G. lacunae Collaboration ideas: Host range tests Increasing phage isolation yield Investigating how to improve growth of phages that produce small plaques

Link to this post | posted 28 Jul, 2022 20:33

kbutela

More of an FYI for the moment for anyone doing autoannotations…Glimmer is currently failing for me on DNA Master as of 7/28/22 at 2 pm, build 2705. Autoannotation throws an error of "could not retrieve gene predictions from server," and nothing will appear in the features window in the dnam5 file. The server is probably down since it was working fine earlier in the week, and I will try again tomorrow.

Link to this post | posted 15 Jun, 2022 13:42
kbutela	Hi all- Does anyone know how to address the issue of DNA Master not entering in submitter information when processing GenBank .sub files? This is a known error that sometimes occurs, but re-processing files isn't fixing the issue for me.

Link to this post | posted 31 May, 2022 14:11

kbutela

Hi all- If you are running the QC flat file checker on the Mac and encounter the error "MMseqs2 not found - please install version 13.45111 and try again" during the checking for database updates stage, you can solve the problem by performing the following. Open a new Terminal window and enter in the following commands conda activate pdm_utils conda install -c bioconda -c conda-forge mmseqs2=13.45111 conda deactivate Close the terminal and try running the flat file checker again. This solution worked for me as of today (5/31/22).

Link to this post | posted 13 Apr, 2022 00:39

kbutela

Hi everyone- The Department of Biological Sciences at the University of Pittsburgh, Pittsburgh Campus is hiring full-time (permanent), full-time visiting, and part-time visiting lab instructors to teach our introductory authentic research-based lab courses beginning in August 2022. Experience in teaching microbiology or physiology labs is a plus but not required. We are also hiring a full-time lecturer to teach Foundations of Biology lecture courses, with microbiology, genetics, or physiology lecture experience as a plus. I would greatly appreciate you passing along this information to any of your contacts who may be looking for a new position, and please feel free to contact me with any questions! Full time lab instructor: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=22002702&tz=GMT-04%3A00&tzname=America%2FNew_York Visiting full time lab instructor: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=22002688&tz=GMT-04%3A00&tzname=America%2FNew_York Part time lab instructor: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=22002689&tz=GMT-04%3A00&tzname=America%2FNew_York Full time lecturer: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=22002782&tz=GMT-04%3A00&tzname=America%2FNew_York

Link to this post | posted 13 Jan, 2022 18:08
kbutela	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. 25Kb

Link to this post | posted 13 Jan, 2022 18:04
kbutela	We use this attached spreadsheet for students to document their notes and conclusions during the annotation process. 102Kb