A list of a =few questions (for my lab-mates):[Please write / skype me, when you can].

• Since the 15th won't work, I'd like to see when I can take vacation, maybe w/some lwop.
  
• nov15, might go to IL for awhile, if that works out?
  
• 
  
• Still not completely sure what RuleEd is doing/outputing; or about ncbo interoperation.
  
• question into Amy how to turn in time; I think I dropped it /between paper&electronic
  
• 
  
• liike the weekly summary, I basically gave up on this page, when I found out no1looks@the main page
  
• 
  
• mon o8, should I come in to meet?
  
• weekend.;I;Found stanford epoch site<=are we connected to this?.
  
• fri o5, =What is kepes going to be used for/could it become a test machine if backed up?
  
• thur oct4, =Could I get a devel.lic for my laptop? We have a site-lic =(actually Why do we have that, do other labs use it as well)?; From sys.htm, here is the dept suggested pdf.-what are thoughts on systems?
  

• wedo3,=I'd like to know how much email people did get from me.
  
• tue o2, .Archesis still live; contact me for login email info via skype.[Linux would be easier to maintain, but can't get it to boot on thesechips anyway.]kepes has poor partitioning (no space errs)&OS tooold for ACL, I'd like to update it. ;from records, no1is actively usingit; does it have a strategic plan?; umlisp on kepes, but no acl on arches yet
  
• mono1,=what are the needs/time-constraints for the (sun/changes) for a new machine decision?. =updated ucsf email, what freq are you getting?
  
• weekend, [amongst the long list of Q's for Ben, is the background researchaffecting design-decisions]&will he 'use' IM now?; simple-fz-rule,code
  
• fri s28,=Was arches ever on the netwrk@this location? Looks like maybe no. I am not ok w/spending more than 1k on these old machines.(even that I think is a waste of$s)vs.a new option machine; Arches online; .. [I have protege&cmucl on it]have acl81 but =where is it's devel.lic?
  
• thur s27, pick up cd-r;try networking&if not a new OS; amia,p
• wed s26, we should all have skype soon; If I'm offline, shoot me an email&I'll start it up.;ccr;rule-testing;comments on the applimatch study<-
  
• tue s25, meeting ;{hope4machine info from Chris then?;&Ben to talk about thecode};Would like to get back2looking@CCR&related.;f-o
  
• mon s24, look over present code for what might be used; how are snomed&other grouping presently becoming CLOS classes? &prot/fztry0(not as nice as rule using lisa.sf.net) {sun feedback from ben}
  
• weekend, look@rules [needed(machine)changes];-any thoughts?,would be great2have some1who would chat; still made a simple rule
  
• fri s21, ..[ps sun still sells ultra's but not sun-blades?]Got info, not worth upgrade, * ..
  
• thur s20, LH meeting 2pm, Found out my ucsf email wasn't getting to DrSim/had a good meeting; Will spec out bug-server =any bugs?, then prep for Tue...
  
• wedn s19,LH meeting postponed; I'm realizing I might not get a history &/ortalks of design; much less an intro; So my work (direction) might nothave as tight a fit as everyone might like @1st. /vmware-deb on pc;*updated*Wiki page(s) *
• tue s18,(*ON* wiki) [hardware is at a stand-still; I'm waiting for sun &/or a new purchase.]
  
• mons19, I asked around about materials, still took awhile
  
• weekend+, went through all the security trainings
• fris14, I'd like to work on protege&talk w/Ben about the rule-work;but he has been offline >1wk(most of my time here);&I'llprobably have to go back in to struggle w/the old/broken? machine(s). [~1st week]
  ...
• thru s13, (long)Orientation,... [SUNis very un-friendly.]We are down on supplies, not even cat5/rj forarches;(given turn-around times for Q&A, I'm going to have to juststart doing things;&look into purchasing..[arches needs OS-upgrade,maybe another HDfix, sun doing some admin; (&/or replacing it is still an option)]
  
• wed s12, clean up bug proj;got some info from simona; ucb-library-day;
  
• tue s11, I can invite the sun-repthis week, but it will be embarassing as I can't log into most of themachines, &so don't have a full idea of what we have. Ben has benunavailable even via email. I'm finding load-lisp.htm to be unusable.[I can't get log in, nor display new files.]We should have one login, w/nfs mounted home-dirs, and be able toeasily get to each machine. I'd rather use a PC now. A bright note: you can open a shared Protege session from the office; So I'lltry this; Which also can be used for editing the kb. [I can add projects thatcan be selected from remotely. *SUMMARY*]
  
• mon s10, goto LH, get id, work on kepes&pc more; try to get other logins &Bens contact info; I'm leaving the PC on for use w/vnc now.
  
• weekend; will installbug-tracking to try it; might put my mockuponline as well mon.;=Does anyone rememberdesign-a-trial? <---***
  
• fri s7, more mail/vpn cfg; mailed sun repr again; would like Ben (phone/person)contact; If we use src-cntrlbug-trac/wiki might be better than bug-zilla;CL-darcs
  
• thur s6, get ncbo wiki &ours...[Also the idea of making explicit dependencies(evenin daily work)is not a bad one.] =What did people think of eligWriter?; <---*******
  
• wedn s5; 1st(partial)group meeting; put vnc on pc(works)&on sun(but blocked);=Need a Ben meeting. Will look@bug-zilla,collabtrac/wiki; If I get the present bug list I can see how well my idea for this works. -
  
• tue sep4, agraph/racerVtb;would like to talk w/Ben about rule-work(as I might start w/this)&get a general overview-soon.
• labor-day-wkend, (more from thu/fri) ..Istill need an overview & some idea when I can get it. I'm hopingfor more on the sets of problems that need to be solved; and how thepresent attempts have evolved to try to meet these changing needs. Thenmore on what the open areas are, & the places where I can help.
  
• fri aug30, ID appt, try to meet w/Ben (when ever he is available); priced-a-mac;(vs. sun)
  Ben will check w/ENS about VPN access again; maybe w/VNC.
  =Has anyone looked@a protege eligibility&umls/etc tabs?
• thur aug29, schedule ID&fingerprints; mention o-device*+;&something like: http://sigswo.org/papers/SIG-SWO-A503/SIG-SWO-A503-03.pdf (though Istill have to say I'd like to stay away from xml/rdf formats until itis absolutely necessary) [noticed no property hierarchy].
  

Some points to look over before(&after) I get in town:

• UMLS
  I have: (from Ben)
  UMLS is the main standardized medical vocabulary that we've used up tothis point for computably representing CT components. NLM's claim isthat UMLS subsumes SNOMED CT, but that seems to be controversial tosome. We aren't necessarily tied to using UMLS over the long term, butwe probably will continue to use something that resembles it, so Ithink becoming familiar with it will be helpful. A good starting pointfor looking at it would be http://www.nlm.nih.gov/research/umls/. Themain documentation page ishttp://www.nlm.nih.gov/research/umls/documentation.html. I think themain thing to get a sense of at first is the overall organization ofthe UMLS data tables and the interrelationships between the three maingroups of tables, META, LEX and NET.

  For a Lisp perspective on UMLS, please look at Kevin Rosenberg'sUMLisp at http://www.cliki.net/umlisp as one way of modeling UMLS inCLOS.

  <QUESTION: I can't find /space/UMLS >The UMLS sources areon rctbank in the /space/UMLS directory. Sad to say, the latest versionof UMLS that's installed now is 2004AB - this is one of the main thingswe need to upgrade. If you find that you need to get a username andpassword to access some code or utils from the NLM site, please let meknow and I'll put you in touch with someone there who can arrange that.Btw, the UMLS sources take up several GB when installed.

  At some point you may also want to subscribe to UMLS list, instructions at [which I have; Also I've loaded the code, but not the data.]

• CL-HTTP (you can start a port on rctbank to work on this) [ask Ben for best current pointers on this]
  It sounded like Ben had a good start on this.
• clinical trials [Simona, can you send some introductory pointers toMichael? Perhaps he’d like to look at OCRe too.] [review RCT Schema,BaT and Presenter code]
  I can look at provided papers, and owl file [also: http://rctbank.ucsf.edu/ontology/outline/index.htm]
  From Simona:
  In terms of introduction to clinical trials, I find the tutorial on theNCI web site quite nice. The drawback is that it is verycancer-focused. However, most concepts are generic and apply to allclinical trials (phase, eligibility, randomization, etc.):

  http://www.cancer.gov/clinicaltrials/resources/basicworkbook/page1

  I also found two short summaries that may be useful.

  http://nextgenmd.org/vol1-4/clinicaltrialsv1i4.html
  http://nextgenmd.org/vol1-5/clinicaltrialsv1i5.html

  Then there is our project web site and you may want to start by looking at the intro page and follow the references.The publication page is not up to date, so I am sending you some recent papers (actually, two papers and a poster description).Finally, this is a recent paper by Ida published on PLoS Medicine:

  http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pmed.0020365&ct=1

  <amia2003_1076.pdf><simtrialbank.pdf><sdarticle-1.pdf>-(mb:I think I once got the Smalltalk code fromChandrasekeran's lab, but have since lost it)

• our various bits of software [upgrade our systems as needed (Ben will let you know)]
  I will start to look around on rctbank.