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

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
>

Received on Monday, 28 May 2012 21:05:55 UTC