Re: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET

I guess I do :)

m.

On Tue, May 29, 2012 at 12:05 AM, Erick Antezana
<erick.antezana@gmail.com>wrote:

> so, do you define 'semantic systems biology' as "an interdisciplinary
> approach to create a more powerful modelling and validation
> framework..."?
>
> cheers,
> Erick
>
> On 28 May 2012 21:41, Michel Dumontier <michel.dumontier@gmail.com> wrote:
> > My goal in pursing semantic systems biology is to i) see to what extent
> > model behaviour can be validated against accrued experimental evidence,
> and
> > ii) that qualitative knowledge can be used to reformulate valid models.
> > Thus, it is an interdisciplinary approach to create a more powerful
> > modelling and validation framework.
> >
> > Best,
> >
> > m.
> >
> >
> >
> >
> > On Mon, May 28, 2012 at 8:16 PM, Franco Du Preez <
> franco.dupreez@gmail.com>
> > wrote:
> >>
> >> Hi Michel,
> >>
> >> Thanks for the questions and references. It would definitely help to
> >> clarify the perceived 'chasm'. In my experience of systems biology,
> >> understanding the control of different cellular processes on the
> behaviour
> >> of the cell/organism has been a central element. Approaches such as
> >> metabolic control analysis provides researchers with a framework to
> reach
> >> this goal, but what would be the analogue of this, if approached from
> the
> >> semantic side? Or is the goal different, to link models to knowledge
> >> frameworks and to make use of automated reasoning instead?
> >>
> >> You also asked wether the approach or application create the chasm. To
> me
> >> the approach is clearly different. In the absence of quantitative
> models, I
> >> would say that the application also differs because its hard to imagine
> how
> >> one would predict the effects of quantitative changes in a system
> without
> >> such models.
> >>
> >> I should also add that the integration of data and models is an
> important
> >> issue at JWS Online and the SEEK, so I am glad to learn more.
> >>
> >> Best regards,
> >> Franco
> >>
> >>
> >> On 25 May 2012, at 4:50 PM, Michel Dumontier wrote:
> >>
> >> Franco,
> >>
> >> On Thu, May 24, 2012 at 10:38 PM, Franco Du Preez
> >> <franco.dupreez@gmail.com> wrote:
> >>>
> >>> Hi all,
> >>>
> >>> As someone speaking purely from the kinetic modeling side, I have to
> >>> admit that there seems to be a quite a big chasm between 'traditional
> >>> systems biology' (if it has existed for a long enough period to be
> called
> >>> that ;)) and the semantic approach.
> >>
> >>
> >> in what what do you think there is a "chasm"? is it just in that the
> >> approaches appear vastly different - one deals with values changing with
> >> time, the other with truth values? Or is it that the applicability seems
> >> unclear? If biomodels database is any indication, one can semantically
> >> annotate the model entities with ontologies without much problem [1]. I
> and
> >> others have shown how to use those ontologies to check the consistency
> of
> >> the models [2]. More recently work [3], shows how we can integrate the
> >> results of simulations in order to answer questions that spans beyond
> the
> >> original model annotations.  There are plenty more things that we can do
> >> now, particularly in the context of enrichment analysis, association
> >> studies, rule mining, etc.
> >>
> >> m.
> >>
> >> [1] http://www.ncbi.nlm.nih.gov/sites/entrez/16333295
> >> [2] http://www.biomedcentral.com/1752-0509/5/124
> >>
> >> [3]
> http://www.slideshare.net/micheldumontier/formal-representation-of-models-in-systems-biology
> >>
> >>
> >>
> >>>
> >>> This being said, I really looked forward to yesterdays session as  it
> >>> touched on the interesting and practical application of model
> alignment, but
> >>> alas, I could not get my audio via the dial in. I guess many must have
> asked
> >>> why were not using skype, so I wont, but Mark's mail has prompted me
> to do
> >>> more digging and I finally got round to downloading a voip client that
> can
> >>> dial sip addresses (holding thumbs for next time).
> >>>
> >>> Cheers,
> >>> Franco du Preez
> >>>
> >>> On 24 May 2012, at 5:18 PM, Mark wrote:
> >>>
> >>> > Hi all SysBio'ers!
> >>> >
> >>> > I know it isn't really my place to be saying anything, but... when
> has
> >>> > that ever stopped me ;-)
> >>> >
> >>> > The last conference call was... odd?...  and while Jun's
> extraordinary
> >>> > efforts to keep it moving forward were greatly appreciated (!!  well
> done
> >>> > !!) I think it might be worth having a very open discussion about
> what our
> >>> > expectations are from this group, since it was a fairly small group
> and
> >>> > apparently with a wide range of experience and expertise.
> >>> >
> >>> > From what I could hear, there were four "tiers" of expertise in the
> >>> > group.  Starting from the bottom:
> >>> >
> >>> > 1)  People like me, who know nothing at all beyond that the
> >>> > SysBio/Modeling community have worked hard on putting together
> standards and
> >>> > technologies that are bearing fruit; and that I (as a mere potential
> user of
> >>> > the tech) need to become MUCH more aware of what they're doing in
> order to
> >>> > successfully pursue my own research interests.  So... I'm the
> ultimate
> >>> > lurker on the call.
> >>> >
> >>> > 2)  People like Erich, who know *a lot* about what's going on in the
> >>> > field (because this is their company's business!) but, as a vendor,
> isn't
> >>> > going to be the first one to speak in a call like this because it
> might
> >>> > come-off sounding like a sales-pitch.  He's likely interested in
> both how
> >>> > the technology is evolving (to ensure their products stay current)
> as well
> >>> > as listening to the needs of the community (so that their products
> stay
> >>> > relevant), but I don't expect him to lead the discussion if for no
> other
> >>> > reason than he's simply too polite to "take-over"  :-)
> >>> >
> >>> > 3)  People like Jun, who has put in a lot of time learning what's out
> >>> > there, has a deep and genuine interest, and wants to discuss the
> pro's and
> >>> > con's of the various pieces at some level of detail with people who
> have at
> >>> > least tried to use it.  (...but there weren't many! ...so she was
> speaking
> >>> > to herself most of the time...)
> >>> >
> >>> > 4)  The full experts in the domain, most of whom were not able to
> make
> >>> > the call, unfortunately.  And I don't say that in any way as an
> accusation,
> >>> > but rather, looking forward, I see a potential "boredom problem",
> which is
> >>> > what I think needs to be discussed.  At least one of the domain
> experts who
> >>> > did attend, left the call mid-chat on the basis that it was "too
> simplistic"
> >>> > (exact quote from IRC)... so if we don't find a way to engage you,
> the
> >>> > experts, we might be in for some disappointing meetings!
> >>> >
> >>> >
> >>> > What I'd like to ask the SysBio community - especially category (4),
> >>> > since it seems to me that they are the critical ones to have on
> these calls,
> >>> > is:  "what can WE (1), (2), (3) do to make these calls as useful to
> you as
> >>> > they will be to us?"  I understand that you're probably already
> talking to
> >>> > each other, since this field is your "baby", and thus these calls
> have the
> >>> > potential to offer you little benefit beyond your existing email
> (etc.)
> >>> > chats!  ...So... what can we do, as the broader-community, to provide
> >>> > value/feedback/etc. that would ensure we all - experts and noobs
> alike - get
> >>> > something useful out of this group and enjoy and value the hour that
> we
> >>> > spend together every couple of weeks?
> >>> >
> >>> > If I'm speaking out-of-turn, please flame me :-)  I can take it!
>  LOL!
> >>> > I just want to see this group succeed, and I am willing to stick my
> neck out
> >>> > to see if I can help!
> >>> >
> >>> > :-)===={
> >>> >
> >>> >   ^^^
> >>> >  my neck
> >>> >
> >>> > Best wishes all!
> >>> >
> >>> > Mark
> >>> >
> >>>
> >>>
> >>>
> >>
> >>
> >>
> >> --
> >> Michel Dumontier
> >> Associate Professor of Bioinformatics, Carleton University
> >> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> >> Group
> >> http://dumontierlab.com
> >>
> >>
> >
> >
> >
> > --
> > Michel Dumontier
> > Associate Professor of Bioinformatics, Carleton University
> > Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> Group
> > http://dumontierlab.com
> >
>



-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com