Link to this post | posted 19 Oct, 2015 16:23
cdshaffer	Dan, Is there anyway to make this post sticky so it stays on top of the list. Might be helpful to new faculty to read this post first and try solutions before posting a question. Could we even change the title to add something like READ THIS FIRST or START HERE. Chris

Link to this post | posted 15 Oct, 2015 21:16
cdshaffer	Ok good to know. I will add this issue to the starterator troubleshooting thread.

Link to this post | posted 12 Oct, 2015 18:57

cdshaffer

It looks like (based on the new 2016SEAVM) that the default database for Starterator is Mycobactriophage_Draft so even if phamerator has Actino_Draft, Starterator may not be using it. To check your instance, open starterator, go to the top magically appearing menu items and select edit-> preferences. In the dialog box, check that the database name in there also set to Actino_draft. It may still be set to Mycobactriophage_Draft. If so, edit that entry to Actino_Draft and hit OK. Once I had done that with my 2016SEAVM I was able to completely process Bipper (great phage name by the way). Also, since I ran the whole phage to check that everything was working with Bipper, I posted the whole phage starterator analysis report as a PDF here. Feel free to download and use if you want. I will figure out how to update the default database for starterator. I don't have direct access to the code for Starterator but I can post a pull request which should fix the issue once it is accepted. That should fix things for future users. Thanks for being the first and discovering the issue of the old default setting for the starterator database. Edited 12 Oct, 2015 21:45

Link to this post | posted 08 Oct, 2015 17:28

cdshaffer

I would be happy to look into this. It is pretty unlikely that you are doing something wrong. To start I need to make sure I have the same database to see if I can replicate the problem. If you open up Phamerator and select Edit -> Preferences. You should see something like the picture I attached. Do you see the same Actino_Draft for the Database, or something else? If you do see Actino_Draft, can you check that your Ubuntu machine is able to get to the internet to download the most recent version of the database? To do that just open up a web browser in the ubuntu machine and see if you can get to sites on the internet like seaphages.org. Edited 08 Oct, 2015 17:33 36Kb

Link to this post | posted 24 Sep, 2015 19:59

cdshaffer

The fasta file from either source will work as input for another program but it can be a hassle if you want to see the sequences yourself. In that case you will probably want to reformat. On the web I use the EMBOSS tool called seqret to do that. Do a google search on "emboss seqret ebi" and pick the seqret server at www.ebi.ac.uk You can upload your fasta file and select "FASTA format" as the output format and all the sequences will be formatted so you can see the entire protein sequence without having to do so much horizontal scrolling.

Link to this post | posted 24 Sep, 2015 19:52
cdshaffer	In DNA Master: 1. DNA Menu, bottom item is "Save ORF's…" which will bring up the tool window 2. You will see a list of all the features in your phage 3. Select one or more by clicking, or use the "Select all genes" button 4. Go to the "Specify Export Files" tab 5. Use the checkboxes as appropriate to control what will be saved (e.g. "Peptide Sequences" 6. Click the "Save" button

Link to this post | posted 18 Sep, 2015 18:03
cdshaffer	Dan, Can you create a page that students can get to that has all the instructions for installing the machine just like on the protected /software/virtualmachine/ page? I would like to be able to point students to all those well written instruction on how to go about installing virtual machines once I give them the virtual disk I want them to use. thanks

Link to this post | posted 17 Sep, 2015 02:10
cdshaffer	Well, I cannot say if we are getting "good" infections. We haven't tried to titer a stock with the different plating techniques. What I can say is every pair of students has a phage from their soil samples. So it seems to be working well enough.

Link to this post | posted 16 Sep, 2015 16:40

cdshaffer

We are using top agar with lividans and getting good plaques. Students are simply spreading phage solution on the plate, then adding top agar onto the plate with the spores already added to the top agar. Very Convenient, since it avoids the 15 min incubation step we did with phage + mycobacteria. Always nice in a class setting with limited time. So far so good for us, looks like we have at least a dozen phage isolated by direct plating. The hard part is growing and collecting the spores it adds time to prep work but they are expected to be stable throughout the phage isolation and purification stage so we only have to collect spores once. Edited 16 Sep, 2015 16:43

Link to this post | posted 11 Sep, 2015 20:45
cdshaffer	Dan, could you post the MD5 hash of the two images. I would like to confirm the integrity of the files after download. Thanks Chris