On a mac here, also having trouble logging in to the VM. Looking more into the keys situation.
On mac, there is this problem: "no support for PKCS#11" Which I'm working to resolve. On Sat, Apr 5, 2014 at 12:15 PM, John Green <john.travis.gr...@gmail.com>wrote: > Thanks Pei. > > > > > Sure, that would be great, add me. > > > > > Jg > > -- > Sent from Mailbox for iPhone > > On Fri, Apr 4, 2014 at 10:15 AM, Chen, Pei <pei.c...@childrens.harvard.edu > > > wrote: > > > John, > > You should have committer rights now... I would suggest opening a Jira > item just so that it can be tracked. > > But you should be able create a subdir within > https://svn.apache.org/repos/asf/ctakes/sandbox and do an svn commit. > > As a side note: ctakes-vm.apache.org has been created now. John, let > me know if you would like to added as list of maintainers. > > We can use that machine to host any of the demo's. > > It requires passwordless ssh so you'll need to ssh-keygen and save them > via http://id.apache.org. > > --Pei > >> -----Original Message----- > >> From: John Green [mailto:john.travis.gr...@gmail.com] > >> Sent: Thursday, April 03, 2014 6:05 PM > >> To: dev@ctakes.apache.org > >> Cc: dev@ctakes.apache.org > >> Subject: RE: ctakes-vm.apache.org > >> > >> Would love to! Ive only submitted those example notes I did though to a > jira > >> ticket. How do I push to the sandbox dir? Any special permissions I > need? > >> > >> > >> > >> > >> JG > >> > >> -- > >> Sent from Mailbox for iPhone > >> > >> On Wed, Apr 2, 2014 at 10:51 PM, Chen, Pei > >> <pei.c...@childrens.harvard.edu> > >> wrote: > >> > >> > John, > >> > If there are no other objections, you can also put it directly in > >> > sandbox https://svn.apache.org/repos/asf/ctakes/sandbox/ > >> > It may make it easier in the future if folks decided to integrate into > >> cTAKES... and possibly save any potential IP/License questions... > >> > --Pei > >> > ________________________________________ > >> > From: John Green [john.travis.gr...@gmail.com] > >> > Sent: Wednesday, April 02, 2014 6:24 PM > >> > To: dev@ctakes.apache.org > >> > Subject: Re: ctakes-vm.apache.org > >> > Great! > >> > Let me clean it up this weekend and ill throw it out onto my github. > Will > >> post link soon; nlt cob this weekend. > >> > JG > >> > -- > >> > Sent from Mailbox for iPhone > >> > On Wed, Apr 2, 2014 at 1:53 PM, andy mcmurry > >> <mcmurry.a...@gmail.com> > >> > wrote: > >> >> Yes! Impeccable timing. Where can we find the python source? > >> >> On Apr 2, 2014 8:33 AM, "John Green" <john.travis.gr...@gmail.com> > >> wrote: > >> >>> Andy: this is very interesting and exciting. > >> >>> > >> >>> > >> >>> > >> >>> > >> >>> I hacked out a script that makes a visually appealing representation > >> >>> of the aggregate pipeline in d3js that, at least for a clinician, is > >> >>> a nice overall summary of the meta data generated from the pipeline. > >> >>> Its really no more than a parser of the xml through the type system > >> >>> spitted out into json, but when I was talking to my informatics > >> >>> department who didnt know much at all about ctakes, it was a great > >> >>> visual summary. Its in python. I dont know if youd want it but it > >> >>> might be worth having the "demo site" spit out a visually appealing > >> >>> graphic like this automatically. If not in python it might be worth > >> >>> adapting it to whatever your using for a platform to spit out the > json for > >> the d3js graphic im using. > >> >>> > >> >>> > >> >>> > >> >>> > >> >>> John > >> >>> > >> >>> -- > >> >>> Sent from Mailbox for iPhone > >> >>> > >> >>> On Thu, Mar 20, 2014 at 5:31 AM, andy mcmurry > >> >>> <mcmurry.a...@gmail.com> > >> >>> wrote: > >> >>> > >> >>> > Yes! I have been working full time on the "apt-get install" task > >> >>> > specific to medical genetics: http://www.ncbi.nlm.nih.gov/medgen > >> >>> > Right now, millions of $$$ are invested in getting phenotype > >> >>> > concepts -- indications, diseases, problem lists -- linked to > >> >>> > patient test results including DNA / RNA / etc. In industry, most > >> >>> > of the curation work is done manually because platforms like > >> >>> > cTAKES are not yet immediately > >> >>> accessible. > >> >>> > I have written code to > >> >>> > A) start automating the installer tasks for cTAKES on Ubuntu 13 > >> >>> > B) install UMLS NLP tools metamap, semrep, semmed > >> >>> > C) mirror NLM content that extends UMLS annotation *SO THAT : * > >> >>> > Mentions of diseases relationships -- SNOMED-CT, HPO, OMIM, GTR, > >> >>> > UMLS -- reference the same semantic relationships in UMLS Clinical > >> >>> > Terms and Genetic Test Reference. This is powerful and all credit > >> >>> > to the NLM for creating MedGen and GTR, new crucial additions to > >> >>> > the UMLS. To my knowledge, these new sources have not been fully > >> >>> > utilized by the medical NLP community. > >> >>> > *I'm strongly advocating for a cTAKES VM that indexes UMLS > >> >>> > concepts in > >> >>> the > >> >>> > same say that NCBI indexes UMLS linked Medical Genetics terms.* > >> >>> > Towards this goal, if other committers are interested, I'm 100% > >> >>> > time committed to this problem. > >> >>> > *TL;DR*: at minimum, having a demo site makes cTAKES more > >> >>> > accessible. We should demonstrate rather than explain every > >> >>> > feature of cTAKES. I'm > >> >>> working > >> >>> > 100% on the Clinical Text +BioNLP problem. If that interests you, > >> >>> > let me know I'm convinced this area has huge, understudied > potential. > >> >>> > --AndyMC > >> >>> > On Tue, Mar 18, 2014 at 8:15 AM, Pei Chen <chen...@apache.org> > >> wrote: > >> >>> >> FYI: > >> >>> >> ASF Infra is setting up our VM for demo purposes. > >> >>> >> INFRA-7451 > >> >>> >> > >> >>> >> If you need access, feel free to let us now. > >> >>> >> Initial maintainers: james-masanz, andymc,chenpei --Pei > >> >>> >> >
