Thank you very much, Ann! It would be great if the "labeling of the data in Genome Graphs" can be addressed as soon, since I am going to demo my session to a big group in a week.
Best regards, Jie -----Original Message----- From: Ann Zweig [mailto:[email protected]] Sent: Monday, November 16, 2009 5:08 PM To: Huang, Jie (NIH/NHLBI) [F] Cc: [email protected] Subject: Re: [Genome] a final round of questions on UCSC GENOME GRAPHS Hello Jie, I will pass along your suggestion for the labeling of the data in Genome Graphs. As for the Session names, you *can* keep the same name after small edits. After you have edited an existing session, simply enter the old name in the "Save current settings as named session:" box, then press submit. You will see an informational box similar to this: This will overwrite the contents of the existing session "SessionName". Proceed? Press "OK" and your new edits will be saved under your old Session name. I hope this information is helpful to you. Please don't hesitate to contact the mail list again if you require further assistance. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Huang, Jie (NIH/NHLBI) [F] wrote: > Hi, Jennifer: > > It is great that you could consider a couple of my proposals as "good idea"! > > If you could pass it on to the development team and somehow they also > consider it as good idea, I would really appreciate is they could accommodate > some small features quick. For example, to display the track name on the left > or on top for the GENOME GRAPHS is something that we eagerly need now and I > hope it won't take long for make such a coding. > > When I created a session, and tell others the session name, then I would like > the session name to stay the same after I made small editing, instead of > sending people new emails saying "here is the new session name". > But I think this is not a big deal. I can just delete the old session name > and save the edited version as the same name. > > Best regards, > Jie > > > ----- "Jie Huang (NIH/NHLBI) [F]" <[email protected]> wrote: > >> From: "Jie Huang (NIH/NHLBI) [F]" <[email protected]> >> To: [email protected], "Jennifer Jackson" <[email protected]> >> Sent: Friday, November 13, 2009 1:46:59 PM GMT -08:00 US/Canada Pacific >> Subject: a final round of questions on UCSC GENOME GRAPHS >> >> please see the attached screenshot of a Genome Graphs session that i >> created. >> >> 1. how to make the track name show on the graph? Right now, the track >> name only shows on the top of the drop-down menu. When I have 10 >> tracks, it would be hard for me to remember which track is what? >> Ideally, the track name should show up to the left of each track >> graph. > > This is very good idea. Tracks are labeled in the Assembly browser in a > similar way (not to the left, but above). I will pass this on to the > scientific development team for consideration. > >> 2. how to change track name? i found that all track names was >> automatically named something like "track name 1" with an appending >> "1". But I really want to change that since users will get confused, >> thinking there might be a "2" or something. > > The track is named when added to the graphing tool (short label). Why they > are numbered I am not exactly sure - I will ask and get back to you. > >> 3. after i open a saved session and make some change, how do save the >> change to this session like how we edit and save a Word document? do i >> have to delete the old session and save it as the same name? >> > > While inside of the original Session, to save the new configuration just save > the same way as for the first round, but give it a new name to preserve both > versions. A Session can have many saved configurations based on the same > underlying data as long as they are named differently. > >> 4. you might be aware of the "Genetic Associations: (NHGRI Catalog)" >> track at Hapmap Browser. However, it is static with just blank dots. >> So, I tried to put the GWAS Catalog into UCSC browser so that users >> can explore interactively. I generated the text file at >> http://people.bu.edu/jiehuang/Catalog.txt and the according UCSC >> browser link is >> http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&hgt.customText=http://people.bu.edu/jiehuang/Catalog.txt >> Can you see if your group might be interested in having something like >> this and make it much better?! > > Another good idea that I will pass on. > >> 5. just to confirm, any named session will be saved for 1 year after >> last use, and any unnamed session will be only saved for 48 hours, >> right? I would not want my named session suddenly disappear after a >> couple of days of inactivity. > > Data (custom track or native) and the browser settings are saved on our > server for an extended period of time when it is in a Session (as opposed to > just a regular Custom Track). It is a bit flexible - we try to keep for at > least a year. However, we do recommend that you download a saved copy of any > session that you would miss if it was lost. Unexpected data loss can occur > (and has occurred) in the past due to server failures. This is rare, but > possible, so it is worth it to be prepared. > >> I realize that you must have a lot to do, and I would really >> appreciate if you could give some quick feedback on these questions. >> >> Best regards & have a wonderful weekend!!! > > You, too! > Jennifer > >> Jie > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
