We are very excited to announce the alpha release of our first JCMS web interfaces (http://jcms-web.jax.org). We would love to get your feedback and hear your discussions and thoughts on this forum thread.
We hope to release an installable web interface package in the next few months. Our initial web interfaces will allow you to run web-based mouse and mating queries on your locally hosted instances of JCMS. We hope to eventually (over the next few years) migrate most or all of JCMS functionality to web interfaces. At this time we'd like to stop and ask you:
When reporting problems, please be sure to let us know what web browser (name and version number) and computer operation system you are using.
Thanks so much in advance.
windows 7, mozilla firefox 3.6.13
it would be helpful if the parameters on the mouse search highlighted when you selected them. then you could see what you had clicked on. i just get an odd blinking effect.
Firefox 3.6.12, Windows 7. Keep in mind we are still using the 3.4.2 version of JCMS, so my responses are based on an older standard.
1) Experimental Plans, Cause of Death Notes, Room
2) I really like the "type in parameter" option for query result filters. I think this is a great tool!
3) It would be better if the query output box was expandable, especially when some results come back as 10-20 pages of 15 rows each.
4) I think the filters should be labelled as "Add" and "Add all" (Not "copy") since the opposite is labelled as "remove". Also, "Copy all" is a little redundant, since you wouldn't need to use the filter if you wanted to include all the possible results, right? Also, when I include "Pen" in the query, the output does not include room number along with the pen number (and health status is missing, although I know that has changed in recent versions of JCMS).
As you click through pages on the query output, the background does a weird flickering up and down thing... which is really distracting. Also, when adding filters from left to right box, the screen moves up and down in the same way.
PS- responses are based on Mouse Query only, Mating Query looked almost identical, nothing jumped out at me as wrong or missing. I didn't go into much detail when looking at Mating Query, either.
This is awesome and I am very excited.
1) The load/save function for queries is going to be an immense help to me since some fields are irrelevant and clicking all those boxes is tedious. Brilliant.
2) I assume the dropdown filters will be labeled so I don't have to open each one to see what it is.
3) I have a suggestion for genotype query. I'd like to be able to see all genotypes for a given mouse and have the results readout one gene per column and sorted by chromosome and Mbp. I've inputted the positions in the gene table already. Is that possible? My current workaround is to put all mouse data into the database and then keep separate genotype Excel files.
4) Finally, how does a web-based interface work as far as accessibility and how it gets installed? I have no experience with this.
Thanks for your comments. A couple of quick responses here.
--- number 3: In the current JCMS mouse query you can get gene's listed in separate columns by checking the box that asks if you would like to "restrict output to selected genes only" We will probably do something similar for the web interface and, yes it should be easy to include position (you could sort by position once it is in excel).
-- number 4: When we release the web interfaces, you'll need to set up a local web server that connects to the database. That is the "hitch" about web interfaces, they require some technical savvy to set up. We'll be trying to make it as simple as possible.
Per number 3: I should clarify that my "genes" are actually microsatellites markers and SNPs, so a single mouse could have around 30 different genotypes. My genotype data ends up looking like this with many more lines in play:
Line 1: chr13=BBBBBBBAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Line 2 chr13=AAAABBBBBBAAAAAAAAAAAAAAAAAAAAAAAAAA
Line 3: chr13=AAAAAAAAAAAAAAAAAAAAAAABBBBBBBAAAAAA
Line 3A: chr13=AAAAAAAAAAAAAAAAAAAAAAAABBBBBAAAAAAA
Line 3AA: chr13=AAAAAAAAAAAAAAAAAAAAAAABBAAAAAAAAAAA
As such, when I do a query I don't know which 10 genotypes to choose, especially if I want to view multiple lines. I also have a huge number of markers to sort through in the dropdown list. I could create some kind of reference sheet, but it would be extensive and cumbersome.
I like the "genotype" result box because it includes all genotype data and I can query every lines at once. The problem is that it sorts "gene" alphabetically and so I have to cross-reference position. If this was sorted by position, it would be fine.
My ideal would be a query result that looks like an import genotype file with chr/Mb in the cells under each gene. I have no problem exporting to Excel and doing a data sort myself, but if the query could do it all it's even better. I may be somewhat unique if most users have transgenic mice and fewer genes, so I don't know that this is a usable idea. I thought I'd throw it out there and see what you think. I am trying to come up with a workaround, but I have no ideas that are functional yet.
Thanks. This is very helpful!
after looking at the forms again, & looking at my list of what the boss expects on a colony report, i noticed that the 'mice in pen' field is missing. it is very helpful to him to see what mice are in the same pen. he also likes to have the parents listed & that seems to be missing too.
Like the way this looks. This will be great for both Mac users and mobile device users. One subtle thing on the query forms. The little dot that tells you what item is selected to be copied into the query is pretty subtle (see red arrow).
I just installed the v. 2.0 web interface on a Mac. It was relatively easy, though I have yet to extensively test it. A couple of very minor things that I ran into that might help others:
1) After running the Installer .jar file the first time, when trying to run the Mysqlscript.cmd, it doesn't work because the explicit location for the mysql binary isn't correct for Macs. the simplest solution is to open the command in a text editor and copy the command line, except for the directory names (starts with /usr/local/bin/, just delete this part and start copying with mysql...) Paste that into the command line and it works fine.
2) the command to start the JBoss instance doesn't work either. This is easily remedied, by going to the directory where the interface was installed and then going into the jcmsJBoss/bin folder and change the permissions on the run.sh file to make it executable. Then just run that shell script and it starts fine.
Two little things I have run into so far. 1) I can't load the Administrator page (calls up a directory named rs that doesn't exist on my system. Not a big deal since all I want to do is change the password for the mtsadmin account.
The other is I have yet to figure out how to access the server from other computers. I'm not sure if this is a firewall issue or what. Will keep you posted if I learn anything else.
Thanks again for doing this. I think it will be very useful in the future.
Thanks for the feedback! I'll see if we can get you questions answered about the admin page soon.
Thanks for the above comments. We need to share those with user community. Initially the installer was designed and tested for windows environment. With above adjustments, we can make it work for Macs.
1) I can't load the Administrator page (calls up a directory named rs that doesn't exist on my system. Not a big deal since all I want to do is change the password for the mtsadmin account.
You should be able to access the Administration page as long as you have
C:\Program Files\The Jackson Laboratory\jcmsJboss\server\default\deploy\jaxLIMS.ear file
jaxLIMS.ear file contains Admin module for the JCMSWeb.
2) In order to access jcmsweb application from remote computers, on windows environment we start the jboss server using -b option
run.bat -b 0.0.0.0. On Mac, probably you can use run.sh -b 0.0.0.0
Genius. #2 worked great. I can now access the database/JCMS from remote computers. #1 has also started working, though I haven't fully figured out why. This time I ran the run.sh (with the -b 0.0.0.0) option as root using sudo. Either, it got over what was keeping it from working, the -b option or jcmsJBoss needs to be run as root, but something in that cocktail even got the administration functions working.
Thanks again and have a great weekend.