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

I think it is a bit generic... the 'semantic' component is missing, see for instance: "Semantic Systems Biology is a complementary approach to Systems Biology which makes use of semantic web technologies to provide biological insights and hypotheses based on biological knowledge that has been adeq

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 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 wrote:

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 wrote: > My goal in pursing semantic systems biology is to i) see to what extent > model behaviour

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

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 a

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

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 meta

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

.@io-informatics.com] Sent: Friday, May 25, 2012 8:30 AM To: Jun Zhao; Michael Miller Cc: Helena Deus; Mark Wilkinson; public-semweb-lifesci@w3.org Subject: RE: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET Dear All, Unfortunately, I won't be able to make the June 6 call either - I

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

kinson; public-semweb-lifesci@w3.org Subject: Re: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET Dear all, Although we didn't have a very productive talk the day before, we managed to provoke some really productive and positive discussions here. This is great! And of course, thanks Mark

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

On 24/05/2012 23:06, Michael Hucka wrote: Hi Jun, Thanks for your mail. Just a quick reply on the following: On Wed, 23 May 2012 13:35:56 +0100, Jun Zhao wrote: Our next meeting will be on June 6. Hope you or your colleagues can make it. http://co.mbine.org/events/HARMONY_2012 looks a very re

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

michael Michael Miller Software Engineer Institute for Systems Biology *From:* Helena Deus [mailto:helenad...@gmail.com] *Sent:* Thursday, May 24, 2012 10:03 AM *To:* Erich Gombocz *Cc:* Mark Wilkinson; public-semweb-lifesci@w3.org; Jun Zhao *Subject:* Re: Reminder: SysBio Wednesday 11AM ET / 4PM

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

Franco, On Thu, May 24, 2012 at 10:38 PM, Franco Du Preez 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 t

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

Hi All,, I'm sorry I couldn't make the call. Sounds like one I would have enjoyed. Re: that 'chasm' between 'traditional systems biology' and the semantic approach - i know it well. there is a 'chasm' within the 'traditional system's biology approach' that doesn't get spoken about (for examp

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

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. This being said, I really looked forwa

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

Hi Jun, Thanks for your mail. Just a quick reply on the following: On Wed, 23 May 2012 13:35:56 +0100, Jun Zhao wrote: > Our next meeting will be on June 6. Hope you or your colleagues can > make it. http://co.mbine.org/events/HARMONY_2012 looks a very > relevant and interesting event. If you

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

2012 10:03 AM *To:* Erich Gombocz *Cc:* Mark Wilkinson; public-semweb-lifesci@w3.org; Jun Zhao *Subject:* Re: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET Hi guys, The fault is entirely mine, I asked Jun to keep the ball rolling as I have not been very present lately due to pr

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

Hi, Just a quick comment. We used to have a Semantic Web / BioPAX workgroup, which probably partially overlaps with the intentions of the W3C Sys Bio Group. The workgroup has been stale for a while, essentially because of a lack of time from who was supposed to organize it... but we just had so

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

Mark, These are very insightful comments - these calls certainly bring together a wide diversity of interests (and personalities ;) - to the point that early exploratory meetings seem rather unstructured (and hence the awkwardness of discourse) - yet, present an opportunity to develop a thought o

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

uminae.com] Sent: Thursday, May 24, 2012 8:18 AM To: public-semweb-lifesci@w3.org; Jun Zhao Subject: Re: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET 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 confere

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

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

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

Dear Michael, It is great to hear from you and very encouraging to see your interest! And thank you for recommending some of the contact points. I believe Nicolas has already come over and give us a presentation a while ago on SBML:) It's a pity that we'll have to miss you in today's call, b

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

Hi Katy, Thanks for letting me know and all the useful pointers! This is an exploratory call. If you spotted anything that we could tie up together with SysMo project please give me a shout. Will be really nice to link up things together! Cheers, Jun On 23/05/2012 11:39, Katy Wolstencroft

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

Hello, I've been meaning to introduce myself to the Systems Biology Task Force for some time, and I apologize for taking so long. As one of the creators of SBML and several other community standardization efforts, as well as having help start BioModels Database itself, you can imagine the topi

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

Hi Jun and all, Apologies, I can't join you today, but it is an interesting topic. On the subject of aligning related models, there is some nice work from Edda Klipp's group that you might want to look at (the makers of Semantic SBML) BMC Bioinformatics.

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

Excellent! Looking forward to it! M On Tue, 22 May 2012 15:27:12 +0200, Jun Zhao wrote: Dear all, I am helping Lena to chair tomorrow's call because she is tied up with travel plans. Tomorrow we are planning to learn more about the MAPK pathway by looking into the BioModels database

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

Dear all, I am helping Lena to chair tomorrow's call because she is tied up with travel plans. Tomorrow we are planning to learn more about the MAPK pathway by looking into the BioModels database, and how to align related models using approaches like Semantic SBML or others. Agenda below: