Link to this post | posted 22 Feb, 2022 16:35
cdshaffer	I heard from Steve, Phamerator is now up and working for me. If it is not working for you be sure to post again.

Link to this post | posted 21 Feb, 2022 18:23
cdshaffer	Not loading for me either. Also 502 error on 2 different browsers. I have sent an email to Steve. Edited 21 Feb, 2022 18:32

Link to this post | posted 18 Feb, 2022 17:30

cdshaffer

I also tell my student to put genbank submissions in a section other than "publications" if they are going to a formal CV since genbank submissions are not really "peer reviewed". I feel like too scientists might object to this as dishonest padding of a CV. I do tell students they should put this on their CV though, as it is important work that deserved recognition (especially for a freshman) so I suggest creating a section called "authored submissions" or "authored contributions". The idea is that we all agree that the work displayed in genbank is important enough that it deserves authorship so it should also be on your CV just don't call it a "publication" and keep that section for authorship on a peer reviewed article (i.e. MRA)

Link to this post | posted 16 Feb, 2022 22:45

cdshaffer

These sound more like generic issues with Win 11 and may not be specific to a version of Win 11 running in a VM. I have not had any chance to work with Win 11 yet, hopefullysomeone who has tried and succeeded at Win 11 installation can help. If all else fails, you can delete the VM and start over. Also note that these virtual systems allow you to create save points which you can go back to (they go by different names, on vitualbox they are called "snapshots". I think they are the same in paralleles. So anyone doing this, take advantage of this snapshot feature. Which is to say, create the VM, install windows, run all updaters, set windows settings as you like, THEN create a snapshot. Now try to install DNA Master, if things gets messed up you can revert back to the snapshot and your windows machine will be exactly like it was before you did any DNA master work. Now you can try something different. Once you get DNA master installed the way you like, create another snapshot, that way if things break in the future you can revert back to the version where DNA Master was successfully installed. wash rinse repeat. Good luck and please, if you find any solutions, post a follow-up here for all of us that will likely be facing these same issues once we migrate to win 11.

Link to this post | posted 16 Feb, 2022 19:01

cdshaffer

Ok I have looked into this more. DNAbinder has an estimated false positive rate of 5-7% when using the "realistic dataset". The biggest issue I don't like is it appears you can only load 1 sequence at a time which makes general use for all genes quite labor and time intensive, not ideal for a good program to recommend everyone use. Also it runs in an old version of PERL and the server is running on Solaris so could be very time consuming to update to a modern server and make it easily usable as a general program (i.e. to make it less labor intensive). DNABIND does allow for multiple submissions, so you could just dump all the protein sequences from a phage in but the program is really designed to analyze 3d structures and the say on the page: " Although it [DNABIND] can predict DNA binding from the protein sequence alone, pure sequence-based prediction was only validated on a very small set of sequences (all of them belonging to structures in the Protein Data Bank)." So there is no way to know its performance with just fasta peptide sequences. The interesting idea would be to combine this program with the newest 3-d predictors and see how it preforms. Again this would be so time consuming I would not recommend using as a general protocol for all phage but a very interesting question that a student could investigate. Bottom line here, I think the issues with practicality mean it should not be added as a recommended protocol for all annotations of all phage but it would be suitable for individual "in depth" investigations. I always have my students do some kind of individual research during the last 3-4 weeks of the semester and using these two programs to search through all the NKF proteins for possible function would certainly qualify for a suitable project. Especially with an eye on specificity and sensitivity issues. I guess the question remains is: should these be used to add the DNA binding to approved annotations when anyone does the work. To me again that would rely on a convincing data analysis showing a very low rate of false positives. Edited 16 Feb, 2022 19:31

Link to this post | posted 16 Feb, 2022 17:42

cdshaffer

I also think that the issue of false positives (i.e. specificity) is as important as Christian's initial investigation into false negatives (sensitivity). So I would like to know if we pick 50 or so phams that we know are NOT dna binding (structural proteins come to mind first, lysis enzymes, holins, suggestions?) for these proteins, do we get any false positives? I always think that keeping a protein NKF is better than giving it a false function. So if no false positives are evident then no major harm would be expected from doing the screen with the two programs and I think it might be worth considering. t If we were to consider I would take the common practice like we do for "membrane proteins" which is we only screen proteins at the end without a better annotation. That is, screen the NKF's at the end for possible "DNA binding" activity. Then only add the annotation "DNA Binding" to the protein if BOTH programs predicted a DNA binding activity. But I will say again that all depends on having an excellent specificity (like 100%). Edited 16 Feb, 2022 18:33

Link to this post | posted 11 Feb, 2022 20:08

cdshaffer

There are two issues here. One is the code and what should starterator put on the report for situations like this. The other is how best to interpret the data to try to come up with the start choice best supported by the evidence. With respect to the former, Amanda is correct in that the code that handles that is quite simple and just is not built to deal with ties and deciding in any formal way how to break them. Coding/testing/publishing changes all takes time so for many issue like this, the question is always "is the problem worth fixing? or "is it good enough even though not perfect?" There are probably dozens of issues like this so there is always more problems that need fixing that time to fix them. Thus, these kinds of issues can be quite common, especially in bioinformatic software where there is one or only a small number of maintainers. This is a good teaching moment to remind students that for all bioinformatic software like this, it is always wise to to be wary of the results from any one program, especially when running across unusual or rare situations. As you use a program more and more you will learn what the program does well and where it "fails" but before that time (to mis-quote an old TV cop show) "Be careful out there". In this particular case, I have time to work on Starterator (pretty much only in the Fall) and I use feedback from users on what issues to fix or new features to add when deciding what exactly to do. So it would be totally appropriate to submit this as an "issue" that needs fixing. This is done on the Github pages where the official version of the code exists. There on github is a discussion board called "issues" where anyone can post bug reports and feature requests. I encourage anyone and everyone to provide feedback there by creating a new issue and posting your requests/comments or adding your own comments to other issues. Any software is only as good as it ability to serve the needs of its users, which is why user feedback is so important. When I get time to work on starterator I go to the issue board to see what's up and any issue with lots of comments is far more likely to be worked on than an issue that is never mentioned. As for the interpretation of Starterator reports during gene start analysis I will leave that for your discussion with Deb.

Link to this post | posted 02 Feb, 2022 05:49

cdshaffer

I would try tie MAC version first both mac and linux have the same unix core structure, you certainly will need to re-install the guest additions though as the mac version will likely have the guest additions for mac installed and you will need to download and install the guest additions for linux. Since you have Mint already installed and running you can do this, I would search for help pages on "how to install virtualbox guest additions on linux guest". Any of the top hits should walk you through the steps. I took a quick look some suggest using the command line, others say the program that automatically runs when you "insert" the virtual CD with the guest additions software works as well. I always used the command line but the autorun could work, as with most things you will just have to try and see. Good luck. Post questions if you get stuck

Link to this post | posted 28 Jan, 2022 18:17

cdshaffer

Unfortunately there are no "good" (i.e. cheap and easy) solutions at this time to getting students access to DNA Master with the newer M1 hardware. I also suspect this is going to be more and more of a problem as Apple moves more and more of their computers to the M1 chips. The best solution at this time is recommend to the student to buy parallels, which is akin to VirtualBox in that it will allow installation and running of Windows Virtual machines. Of course the instructions for doing this are all for virtualbox and so many exact details on installation and running of the windows machine will differ slightly with parallels. The only good news there is really is that there is a 50% discount for students for the basic version of parallels, point the student to this page for all the details: https://www.parallels.com/landingpage/pd/education/ As a final note I will say that the minimum recommended specifications for Parallels is quite low and I would expect most users with that bottom of the line computer to have a very unsatisfactory experience. I would tell my students not to bother spending $40 for parallels unless they have AT LEAST 8 gig of memory, less than that it is just wouldn't be worth the price.

Link to this post | posted 18 Jan, 2022 23:56

cdshaffer

Has anyone tried buying cloud PC access? You can use these search term: "windows cloud PC" or "Desktop as a Service" to see what I am talking about. All these are paid services (although some do have a free period to start), and unfortunately most are designed for businesses not individuals but there are some out there that do cater to the individual. These systems are designed such that a student could connect remotely from any computer with a browser (like a chromebook). The total cost would likely be less than the cost of a typical text book will vary quite a bit depending on how powerful a machine you need. Dan, can you tell us what is the bare minimum one would need for running DNA Master in Windows 10? I assume a student could get by with 1 vCPU but how much memory? This would help estimate prices. Any reports from others that might have tried this, would appreciate if you could tell us of your experience.