14:38:58 <RRSAgent> RRSAgent has joined #HCLS
14:38:58 <RRSAgent> logging to http://www.w3.org/2012/03/14-HCLS-irc
14:44:21 <Lena> zakim, list
14:44:21 <Zakim> I see Team_(ia)14:02Z, WAI_RDWG()10:30AM, WF_(AC)9:00AM, Team_(crm)14:06Z, Team_(validator)14:02Z active
14:44:24 <Zakim> also scheduled at this time are Team_W3M()8:00AM, Team_(PH Cadence)10:30AM, WAI_Team(WAIT)10:30AM, IA_Fonts()10:00AM, UW_DAP()10:00AM
14:46:11 <ericP> heya lena
14:46:31 <ericP> it appears i never made a res for this meeting
14:46:37 <ericP> there's nothing after it, is there?
14:47:27 <ericP> how many folks do you expect?
14:48:37 <Lena> shall we openup for 10?
14:48:56 <ericP> sure, we can shoot higher, just in case
14:49:02 <Lena> ok,.... 20?
14:49:19 <Lena> nothing after this, I think
14:49:22 <ericP> let's say 15, in order not to alarm others
14:49:39 <ericP> Zakim, space for 15 for 90 mins?
14:49:41 <Zakim> sorry, ericP; could not schedule an adhoc conference; passcode overlap; if you do not have a fixed code you may try again
14:49:47 <ericP> hmm
14:51:37 <ericP> lodd was scheduled from 15-1600Z
14:51:49 <ericP> Zakim, list?
14:51:49 <Zakim> I don't understand your question, ericP.
14:51:55 <ericP> Zakim, list
14:51:55 <Zakim> I see Team_(ia)14:02Z, WAI_Team(WAIT)10:30AM, WAI_RDWG()10:30AM, WF_(AC)9:00AM, Team_(crm)14:06Z, Team_(validator)14:02Z active
14:51:58 <Zakim> also scheduled at this time are Team_W3M()8:00AM, Team_(PH Cadence)10:30AM, SW_RDFWG()11:00AM, IA_XForms()11:00AM, SW_HCLS(LODD)11:00AM, IA_Fonts()10:00AM, UW_DAP()10:00AM,
14:51:58 <Zakim> ... I18N_CoreWG()11:00AM
14:52:19 <ericP> i guess the list changes at 10mins to the hour
14:52:47 <ericP> there won't be an LODD, will there?
14:53:23 <ericP> doesn't matter
14:53:26 <ericP> Zakim, this will be lodd
14:53:26 <Zakim> ok, ericP; I see SW_HCLS(LODD)11:00AM scheduled to start in 7 minutes
14:53:45 <ericP> Wednesdays 15:00-16:00 UTC (11:00am-12:00pm Boston local)
14:53:45 <ericP> Zakim Bridge +1.617.761.6200, conference 4257 ("HCLS")
14:53:45 <ericP> 15 participants
14:54:30 <YolandaGil> YolandaGil has joined #HCLS
14:55:19 <Zakim> SW_HCLS(LODD)11:00AM has now started
14:55:26 <Zakim> +[ISI]
14:55:53 <Zakim> +[IPcaller]
14:55:55 <YolandaGil> Hi Lena and all!
14:56:01 <YolandaGil> Slides are at http://www.isi.edu/~gil/slides/W3C-SystemsBiologyTF-14March2012.pdf
14:56:56 <bbalsa> bbalsa has joined #HCLS
14:56:56 <markw> markw has joined #hcls
14:56:57 <bttb> bttb has joined #hcls
14:57:07 <Zakim> -[IPcaller]
14:58:45 <jun> jun has joined #hcls
14:58:59 <ericP> heya YolandaGil 
14:59:07 <Zakim> +bosse
14:59:14 <ericP> sorry i'll miss your talk. will be on another telecon
14:59:19 <Zakim> +Lena
15:00:00 <michael> michael has joined #hcls
15:00:42 <Zakim> + +1.703.983.aaaa
15:00:53 <laleh> laleh has joined #HCLS
15:00:59 <Zakim> + +1.206.732.aabb
15:01:05 <Zakim> +??P30
15:01:11 <jun> zakim, ??P30 is me
15:01:11 <Zakim> +??P32
15:01:19 <oliver> oliver has joined #hcls
15:01:23 <Zakim> +jun; got it
15:01:26 <jun> Hi lena
15:01:28 <Lena> is the echo gone?
15:01:31 <oliver> hi
15:02:31 <Zakim> +[IPcaller]
15:02:39 <MacTed> MacTed has joined #hcls
15:04:04 <Zakim> + +1.617.818.aacc
15:04:13 <Lena> https://deri.webex.com/deri/e.php?AT=WMI&EventID=204980932&PW=2848010d052822202b35&RT=MTgjMjE%3D
15:05:23 <Lena> slides: http://www.isi.edu/~gil/slides/W3C-SystemsBiologyTF-14March2012.pdf
15:05:34 <CGI448> CGI448 has joined #HCLS
15:05:43 <oliver> zakim, who is there
15:05:43 <Zakim> I don't understand 'who is there', oliver
15:05:51 <oliver> zakim, help
15:05:51 <Zakim> Please refer to http://www.w3.org/2001/12/zakim-irc-bot for more detailed help.
15:05:53 <Zakim> Some of the commands I know are:
15:05:53 <Zakim>  xxx is yyy       - establish yyy as the name of unknown party xxx
15:05:53 <Zakim>                     if yyy is 'me' or 'I', your nick is substituted
15:05:53 <Zakim>  xxx may be yyy   - establish yyy as possibly the name of unknown party xxx
15:05:53 <Zakim>  I am xxx         - establish your nick as the name of unknown party xxx
15:05:54 <Zakim>  xxx holds yyy [, zzz ...] - establish xxx as a group name and yyy, etc. as participants within that group
15:05:56 <Zakim>  xxx also holds yyy - add yyy to the list of participants in group xxx
15:05:58 <Zakim>  who's here?      - lists the participants on the phone
15:06:00 <Zakim>  who's muted?     - lists the participants who are muted
15:06:02 <Zakim>  mute xxx         - mutes party xxx (like pressing 61#)
15:06:04 <Zakim>  unmute xxx       - reverses the effect of "mute" and of 61#
15:06:06 <Zakim>  is xxx here?     - reports whether a party named like xxx is present
15:06:08 <Zakim>  list conferences - reports the active conferences
15:06:10 <Zakim>  this is xxx      - associates this channel with conference xxx
15:06:13 <Zakim>  excuse us        - disconnects from the irc channel
15:06:14 <oliver> zakim, who's here?
15:06:15 <Zakim> I last learned something new on $Date: 2012/02/01 21:15:02 $
15:06:18 <Zakim> On the phone I see [ISI], bosse, Lena, +1.703.983.aaaa, +1.206.732.aabb, jun, ??P32, [IPcaller], +1.617.818.aacc
15:06:27 <Zakim> On IRC I see CGI448, MacTed, oliver, laleh, michael, jun, bttb, markw, bbalsa, YolandaGil, RRSAgent, Zakim, Lena, matthias_samwald, egonw, vlmir4irc, ericP
15:06:44 <ericP> oliver, who is here?
15:06:59 <markw> What is the WebEx password?
15:06:59 <ericP> Zakim, who is here?
15:06:59 <Zakim> On the phone I see [ISI], bosse, Lena, +1.703.983.aaaa, +1.206.732.aabb, jun, ??P32, [IPcaller], +1.617.818.aacc
15:07:01 <Zakim> On IRC I see CGI448, MacTed, oliver, laleh, michael, jun, bttb, markw, bbalsa, YolandaGil, RRSAgent, Zakim, Lena, matthias_samwald, egonw, vlmir4irc, ericP
15:07:10 <oliver> zakim, +1.617.818.aacc is oliver
15:07:10 <Zakim> +oliver; got it
15:07:27 <Lena> zakim, who is making noise?
15:07:35 <Lena> Zakim, who is making noise?
15:07:38 <Zakim> Lena, listening for 10 seconds I heard sound from the following: Lena (1%), ??P32 (4%), oliver (74%)
15:07:46 <oliver> zakim, mute me
15:07:46 <Zakim> oliver should now be muted
15:07:49 <Zakim> Lena, listening for 10 seconds I heard sound from the following: [ISI] (9%), Lena (18%), +1.703.983.aaaa (4%), ??P32 (9%), +1.206.732.aabb (5%), oliver (19%)
15:08:08 <Lena> http://www.w3.org/wiki/HCLSIG/SysBio/20120314
15:08:38 <Lena> slides: http://www.isi.edu/~gil/slides/W3C-SystemsBiologyTF-14March2012.pdf
15:09:58 <jun> Are we using IRC for scribing?
15:11:44 <HelenaDeus> HelenaDeus has joined #hcls
15:11:54 <HelenaDeus> YolandaGil: characteristics of the data are often lost
15:12:33 <HelenaDeus> YolandaGil: metadata not preserved when moved from one application ot the next
15:13:09 <HelenaDeus> YolandaGil: detective work to figure out where the data came from
15:13:58 <HelenaDeus> YolandaGil: important to mine the metadata as we process it
15:15:52 <Guest> Guest has joined #hcls
15:16:40 <HelenaDeus> YolandaGil: in wings, metadata is used in several ways, e.g. set parameters
15:18:09 <HelenaDeus> YolandaGil: 3 different ways to doa certain step - how to choose one dinamically?
15:18:28 <Zakim> -Lena
15:18:58 <Zakim> +Lena
15:19:33 <HelenaDeus> YolandaGil: wings wil dynamiclly adapt the model according to the input data
15:19:47 <HelenaDeus> YolandaGil: this is possible because karma + wings are provenance awarre
15:21:11 <HelenaDeus> YolandaGil: (slide 8)
15:21:55 <HelenaDeus> YolandaGil: in wings, every workflow has a data flow - every component has a variable associated with it, which means we can add contrains
15:23:03 <HelenaDeus> YolandaGil: all this is done using rdf and owl and making full use of sem web technologies
15:23:19 <dgarijo> dgarijo has joined #HCLS
15:23:25 <Zakim> -Lena
15:24:13 <Zakim> +Lena
15:24:52 <HelenaDeus> YolandaGil: slide 11 
15:25:14 <Zakim> +??P24
15:25:41 <dgarijo> Zakim, ??P24 is me
15:25:41 <Zakim> +dgarijo; got it
15:26:15 <HelenaDeus> YolandaGil: using propagation to find workflows (e.g. based on some type of data or using some algorithm)
15:26:35 <esteban> esteban has joined #hcls
15:26:42 <HelenaDeus> YolandaGil: slide 12
15:28:53 <HelenaDeus> YolandaGil: slide 17 - image analysis
15:30:15 <HelenaDeus> YolandaGil:  slide 18 - workflow sharing
15:30:21 <HelenaDeus> YolandaGil: population genomics 
15:30:32 <stuartowen> stuartowen has joined #hcls
15:30:55 <HelenaDeus> YolandaGil: slide 19 - using constrains on the different components
15:32:30 <HelenaDeus> YolandaGil: slide 20 - finding out how reproducible the results from research are
15:33:13 <HelenaDeus> YolandaGil: duerr et al science 2006
15:33:27 <HelenaDeus> YolandaGil: using an open workflow, the results are made reproducible
15:34:13 <HelenaDeus> YolandaGil: slide 21 - using more modern algorithms, was able to reproduce the results by replicating the workflow
15:35:36 <FrancoduPreez> FrancoduPreez has joined #hcls
15:36:00 <HelenaDeus> YolandaGil: slide 23 - replicated workflow for drug discovery (based on kinnings et al 2010) 
15:36:35 <HelenaDeus> YolandaGil: same workflow should be applicatble to other diseases
15:37:51 <HelenaDeus> YolandaGil: slide 24 - problems: people have different prefernces on which code to use
15:38:09 <HelenaDeus> YolandaGil: so wings is independent of the computational statistics platform
15:38:34 <HelenaDeus> YolandaGil: slide 25 - worflow publication is abstract; also published as links data
15:39:18 <HelenaDeus> YolandaGil: slide 28 - developed extension to OPM to describe workflows
15:39:33 <HelenaDeus> YolandaGil: soon going to develop an extension to prov standard!
15:40:12 <HelenaDeus> YolandaGil: slide 29 - everything in the workflow end us as linked data with links for the source code, the datasets, etc
15:41:15 <HelenaDeus> YolandaGil: slide 32 - high school students can use it to do productive work!
15:43:01 <HelenaDeus> YolandaGil: discovery informatics - extending data with semantic models reprsentation, data discovery, etc
15:43:59 <Lena> carole: data in mexperiment?
15:46:44 <Lena> michael: in myexperiment, we are tied to the application to run it again - how to make that more general?
15:47:42 <Lena> carole: workflow4ever - represening workflows as a part of great collection
15:48:00 <Lena> carole: share provenance execution logs (myexperiment 2.0)
15:49:12 <Lena> YolandaGil: when the workflows are exported, code is made available
15:51:29 <Lena> carole: workflows for systems biology? (e.g. model validation)
15:53:20 <Lena> jun: very expensive to replicate workflows/set up the services for the worflow
15:53:33 <ericP> Zakim, please dial ericP-office
15:53:33 <Zakim> ok, ericP; the call is being made
15:53:35 <Zakim> +EricP
15:53:39 <Lena> jun: if we want to use wings, how much effort would be involved?
15:54:20 <Lena> YolandaGil: 3 mo of work 
15:54:52 <oliver> oliver has joined #hcls
15:54:54 <Lena> YolandaGil: biologist may take longer
15:55:23 <Zakim> - +1.703.983.aaaa
15:58:20 <Lena> YolandaGil: correction - 3 mo for the drugs project; high school kids have it running in 1 day!
16:01:13 <Zakim> -[IPcaller]
16:01:42 <Lena> YolandaGil: software interoperability by creating class of components
16:02:06 <er> er has joined #hcls
16:06:45 <dgarijo> I am here, I can listen to you!
16:08:33 <Zakim> - +1.206.732.aabb
16:09:04 <Zakim> -EricP
16:09:05 <Zakim> -[ISI]
16:09:06 <Zakim> -bosse
16:09:07 <Zakim> -dgarijo
16:09:09 <Zakim> -Lena
16:09:10 <Zakim> -jun
16:09:19 <Zakim> -??P32
16:09:24 <Lena> RRSAgent: please draft the minutes
16:09:24 <RRSAgent> I have made the request to generate http://www.w3.org/2012/03/14-HCLS-minutes.html Lena
16:09:26 <Zakim> -oliver
16:09:28 <Zakim> SW_HCLS(LODD)11:00AM has ended
16:09:28 <Zakim> Attendees were [ISI], [IPcaller], bosse, Lena, +1.703.983.aaaa, +1.206.732.aabb, jun, oliver, dgarijo, EricP
16:09:34 <Lena> RRSAgent: please make minutes world-visible
16:09:34 <RRSAgent> I'm logging. I don't understand 'please make minutes world-visible', Lena.  Try /msg RRSAgent help
16:09:57 <ericP> RRSAgent, please make log world-visible
16:10:18 <Lena> thanks, eric
16:10:31 <ericP> quite welcome
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