Santa Fe Institute Events Wiki - User contributions [en]

Cellular Slime Mold Simulation

2007-06-18T03:02:05Z

Natasha: /* Reading material */

{{CSSS 2007 Santa Fe}}
= News =
'''Next meeting Monday 061807, 4.30 pm.'''

* 061407 Meeting today '''after the lecture at 8 pm'''. Place: Cafeteria first floor Peterson Student Center /Johan

* 061107: I've developed a simple graphical viewer that does the job of displaying the individual CA cells, color coded the same way as in the article. It's not great, but if anyone is interested, let me know and I'll make the code avaliable. /Johan

* Meeting on Thursday the 14th before dinner

= Old news =
First meeting will be on '''Monday the 11th at 6 pm'''. Lets meet '''outside the dining room'''. "Homework" till then will be to read the original article(see list below) and think a little of what we want to get out of the project. /Johan

= Background =
One of the most widely studied and relatively simple organisms in which to study morphogenesis (the shapes of organisms and the positions in the organisms of various specialized cell types) is the so-called cellular slime mold. It provides a simple model organism for studying many general developmental processes, including chemotaxis (behavioral response by an organism to a directional chemical stimulus), cell sorting, pattern formation and complex behavior through self-organization.

Normally, slime mold is a unicellular amoeba, but when food resources become scarce, they aggregate and form multicellular organisms that can move towards food sources.

= Proposition =
There is an article by N. J. Savill and P. Hogeweg where a model of the morphogenesis of these slime mold organisms is presented. What amazes me with this article is that the model seems to be relatively simple, but that it can still account for the whole morphogenetic process from single cells to a larger aggregate of cells, and finally to a multicellular organism capable of coordinated motion.

I propose a project group for implementing this model and possibly extend it in directions that we find suitable. I’m sure some very interesting questions will pop up along the way.

= More about the model =
The simulations are based on a cellular automata (CA) model, where each amoeba is represented as a collection of CA cells. A Monte Carlo simulation is performed, where amoebae of different types have a tendency to group together. This results in a cell sorting behavior. Another mechanism in the model is communication between amoebae via cAMP (cyclic adenosine monophosphate) chemicals, modelled by a partial differential equation. This results in aggregation of the amoebae into a ”multicellular organism” (interesting philosophical/biological question if this really counts as a multicellular organism). Without any change of parameters, the slime mold eventually starts to move guided by cAMP waves. The whole process seems to very much resemble what happens for living slime mold.

= Participants =
* Johan Nyström (nystjoha@chalmers.se)
* Will Ludington
* Tim Johann
* Ryan Chisholm
* Dan Lester - maybe before we get together on monday, have a think about scope for this project, especially something of biological importance
* Natasha - I would like to know the date and time of meeting.
* (add your name here)

= Reading material =
'''On the Cellular Automaton model:'''
* Original article: [http://homepages.ed.ac.uk/nsavill/Papers/dicty.pdf]
* A continuation of the original article: [http://www-binf.bio.uu.nl/pdf/Maree.jtb99-199.pdf]. Have a look at picture 2 on page 7. They make their slime mold follow a thermal gradient.
* ''Computing an organism: on the interface between informatic and dynamic processes'', P. Hogeweg, Biosystems 64 (2002) 97-109: This article contains an overview of the work done using the model.
* ''How amoeboids self-organize into a fruiting body: multicellular coordination in Dictyostelium discoideum'' Proc. Natl. Acad. Sci. USA 98 (7), 3879-3883
'''Biologically relevant articles:'''

If someone know any article, please add it here.

I suggest the following reading material(Natasha)
* Try the following links for some biologically relevant articles:
http://www.mycologia.org/cgi/content/full/97/1/178 (Behavior of cellular slime molds in the
soil)
http://www.ucmp.berkeley.edu/protista/slimemolds.html (Introduction to the slime molds)
http://www.ias.ac.in/jbiosci/march1999/99bc
http://www.biolbull.org/cgi/reprint/122/1/13 (Aggregation of territories in the cellular
slime molds)
jcs.biologists.org/cgi/reprint/22/1/41.pdf (CYCLIC ADENOSINE MONOPHOSPHATE AND THE
DEVELOPMENT OF POLYSPHONDYLIUM)
* For comprehensive information on Dictyostelium discoideum, visit http://dictybase.org/
For an overview of world-wide research on D.discoideum,visit http://dictyworkbench.sdsc.edu/
For some kool videos of Dicty, try http://dictybase.org/Multimedia/index.html
* And the comprehensive one: A Cellular Automata model for D.Discoideum (http://www.cs.york.ac.uk/ftpdir/reports/YCS-2005-393.pdf)
Phototaxis during the slug stage of Dictyostelium discoideum: a
model study (http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1690080&blobtype=pdf)

'''Other'''

...

Cellular Slime Mold Simulation

2007-06-18T02:55:44Z

Natasha: /* Reading material */

{{CSSS 2007 Santa Fe}}
= News =
'''Next meeting Monday 061807, 4.30 pm.'''

* 061407 Meeting today '''after the lecture at 8 pm'''. Place: Cafeteria first floor Peterson Student Center /Johan

* 061107: I've developed a simple graphical viewer that does the job of displaying the individual CA cells, color coded the same way as in the article. It's not great, but if anyone is interested, let me know and I'll make the code avaliable. /Johan

* Meeting on Thursday the 14th before dinner

= Old news =
First meeting will be on '''Monday the 11th at 6 pm'''. Lets meet '''outside the dining room'''. "Homework" till then will be to read the original article(see list below) and think a little of what we want to get out of the project. /Johan

= Background =
One of the most widely studied and relatively simple organisms in which to study morphogenesis (the shapes of organisms and the positions in the organisms of various specialized cell types) is the so-called cellular slime mold. It provides a simple model organism for studying many general developmental processes, including chemotaxis (behavioral response by an organism to a directional chemical stimulus), cell sorting, pattern formation and complex behavior through self-organization.

Normally, slime mold is a unicellular amoeba, but when food resources become scarce, they aggregate and form multicellular organisms that can move towards food sources.

= Proposition =
There is an article by N. J. Savill and P. Hogeweg where a model of the morphogenesis of these slime mold organisms is presented. What amazes me with this article is that the model seems to be relatively simple, but that it can still account for the whole morphogenetic process from single cells to a larger aggregate of cells, and finally to a multicellular organism capable of coordinated motion.

I propose a project group for implementing this model and possibly extend it in directions that we find suitable. I’m sure some very interesting questions will pop up along the way.

= More about the model =
The simulations are based on a cellular automata (CA) model, where each amoeba is represented as a collection of CA cells. A Monte Carlo simulation is performed, where amoebae of different types have a tendency to group together. This results in a cell sorting behavior. Another mechanism in the model is communication between amoebae via cAMP (cyclic adenosine monophosphate) chemicals, modelled by a partial differential equation. This results in aggregation of the amoebae into a ”multicellular organism” (interesting philosophical/biological question if this really counts as a multicellular organism). Without any change of parameters, the slime mold eventually starts to move guided by cAMP waves. The whole process seems to very much resemble what happens for living slime mold.

= Participants =
* Johan Nyström (nystjoha@chalmers.se)
* Will Ludington
* Tim Johann
* Ryan Chisholm
* Dan Lester - maybe before we get together on monday, have a think about scope for this project, especially something of biological importance
* Natasha - I would like to know the date and time of meeting.
* (add your name here)

= Reading material =
'''On the Cellular Automaton model:'''
* Original article: [http://homepages.ed.ac.uk/nsavill/Papers/dicty.pdf]
* A continuation of the original article: [http://www-binf.bio.uu.nl/pdf/Maree.jtb99-199.pdf]. Have a look at picture 2 on page 7. They make their slime mold follow a thermal gradient.
* ''Computing an organism: on the interface between informatic and dynamic processes'', P. Hogeweg, Biosystems 64 (2002) 97-109: This article contains an overview of the work done using the model.
* ''How amoeboids self-organize into a fruiting body: multicellular coordination in Dictyostelium discoideum'' Proc. Natl. Acad. Sci. USA 98 (7), 3879-3883
'''Biologically relevant articles:'''

If someone know any article, please add it here.
I suggest the following reading material(Natasha)
* Try the following links for some biologically relevant articles:
http://www.mycologia.org/cgi/content/full/97/1/178 (Behavior of cellular slime molds in the
soil)
http://www.ucmp.berkeley.edu/protista/slimemolds.html (Introduction to the slime molds)
http://www.ias.ac.in/jbiosci/march1999/99bc
http://www.biolbull.org/cgi/reprint/122/1/13 (Aggregation of territories in the cellular
slime molds)
jcs.biologists.org/cgi/reprint/22/1/41.pdf (CYCLIC ADENOSINE MONOPHOSPHATE AND THE
DEVELOPMENT OF POLYSPHONDYLIUM)
* For comprehensive information on Dictyostelium discoideum, visit its database
http://dictybase.org/
For an overview of world-wide research on D.discoideum,visit http://dictyworkbench.sdsc.edu/
For some kool videos of Dicty, try http://dictybase.org/Multimedia/index.html
* And the comprehensive one: A Cellular Automata model for
Dictyostelium Discoideum (http://www.cs.york.ac.uk/ftpdir/reports/YCS-2005-393.pdf)
Phototaxis during the slug stage of Dictyostelium discoideum: a
model study (http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1690080&blobtype=pdf)

'''Other'''

...

CSSS 2007 Santa Fe-After Hours

2007-06-15T05:39:06Z

Natasha: /* Bandelier Nat'l Monument/Frijoles Canyon Trail/Los Alamos */

{{CSSS 2007 Santa Fe}}

==Anyone for Bridge?==
* I realise this may be betraying my inner geek a little too much, but I was just wondering if anyone at the school was interested in getting together for a bit of just-for-fun bridge? If enough people are interested, then maybe we could organise a regular evening while we're here. It's a great game and should appeal to all complexity students! (9 out of 10 Grandmothers can't be wrong......!) Any takers, just get in touch with me! [[http://www.santafe.edu/events/workshops/index.php/Kernuack Hannah]]
You are a geek. I like playing 500. I would be up for learning Bridge if people are patient. [Ryan]

Have to admit that I played some bridge a loooong time ago... forgotten most about it by now though. But I'm willing to give it a shot (hope for your own sake that you're better in bridge than in pool Hannah ;D) [Johan]

its time to face facts: we all are geeks (you too have been tainted with this brush ryan!) and should be wallowing in it. can this session be titled "everything you ever wanted to know about bridge but were too afraid to ask?" if so, I am in [dan]

I'm sure I can manage to articulate the basics to a willing audience ;o) Hannah

- should we try for a further "refinement" on sunday evening? cheese and port?? [dan]

I know I missed the boat on the first night but I would like to learn this rule-filled game properly. I've played a couple of times many years ago so perhaps some cheese and port will jog my memory [[http://www.santafe.edu/events/workshops/index.php/Alex_Healing Alex]]

==Monday, June 11==
===7:00 soccer=== perhaps low attendance due to the Matlab tutorial.

==Tuesday, June 12==
===6:30 ultimate=== @ soccer fields

==Wednesday, June 13==
===morning bird/wildlife walk=== Are you getting too much sleep? Do your days feel empty? Join us for a morning bird/wildlife walk. The general plan is to be on the trail by 6:00 am and return before the end of breakfast. If we have enough vehicles, the Audubon center at the end of Upper Canyon Road (just a few minutes' drive, no dogs allowed [http://www.audubon.org/chapter/nm/nm/rdac/audubon_center/rdnature/natural_history.html link]) is probably our best option. If we don't have transportation, we'll just head up the trail near campus. Fred and I both have binoculars that can be shared, but if anyone else has a pair they can lend to the endeavor, that'd be great. I'll post more details as the week progresses and we get a better idea of who's coming. Drop me a line or leave your name below if you're interested. [[http://www.santafe.edu/events/workshops/index.php/James_Battin James]](james.battin at noaa.gov)
===Join us for "Music on the Hill" at St. Johns college from 6-8pm=== for food and drink; this Wed is '''Southwest Jazz Orchestra''' by Big Band Jazz. For more info see, [http://www.stjohnscollege.edu/asp/main.aspx?page=6981 schedule here].
===7:00 soccer===

There is a concert on the soccer fields tonight, so we have to move the game.

The GAME IS ON. We're playing down on the fields by the public school on Camino de Cruz Blanca. Turn left out the front entrance of St. John's and left again. The fields will be on your right. It's a short walk from St. John's.

We'll play from 7:00 till dark, unless everyone goes to Rockmore's lecture.

Ben

===7:00 Getting Older... El Farol....=== the inevitable is looming large & I am once again "getting older". I will be marking expiration of my 30th year with traditional comiseratory drinks at el foral & all and sundry are welcome to chastise and deride. it will be a great night!! will be leaving st johns around 7, love to see you there, cheers,

old man dan

I hate to be the one to break this to you, but I think it is actually the end of your 31st year... I will be there to celebrate.

Ryan.

I can drive revelers over to the bar from Dan Rockmore's lecture - do you think you will still be there around 9:30 or 10P?? --Mollie

Actually I am planning on making Dan R's lecture too so I plan to be at El Farol from 9pm-ish onwards - of course, roll down for a drink beforehand if you want too!! cheers

dan (l)

I'll see if I can rally the soccer guys to head out after our game. --Ben

==Thursday, June 14==
===Food and drink at "Cowgirls" on Guadalupe from 6-?===
===6:30 ultimate @ soccer fields===
===6:15 cricket (near soccer fields if there is space and enough interest). ===

==Saturday, June 16==
===Climbing excursion=== We'll be going back to [[http://www.geocities.com/Yosemite/Trails/9507/lasconchas.htm Las Conchas]] or in the Sandias doing some trad/gear routes. Vikas, Josh, Kath, Olaf, Andy (?), elise (if there is space)

===Bandelier Nat'l Monument/Frijoles Canyon Trail/Los Alamos=== Anyone interested in hiking the frijoles canyon trail to the bandelier nat'l monument? The monument is a group of ancient ruins/caves/etc and supposed to be beautiful (and a quick drive). The Frijoles Canyon Trail is an "easy walk" to the ruins. It's also really close to Los Alamos... Heather (hbeil at email.unc.edu).

I'm interested. Monika (monika at mimuw.edu.pl)

Me too. Mike W.

Sounds like a nice trip, I'll join you :-) /Johan

Me too, plus I have a car, if needed. -Chris

I'd like to go on a hike this weekend, count me in if it's just a day trip -Alex (alexhealing (at) gmail.com)

I'd like to join the group also. -Natasha

==Sunday, June 17==
whitewater rafting in the taos box canyon.

* note: this event is now closed.

==june 16/17 - Overnight Hike Moved==

Andrew - perhaps its better to put some more thought into this and do it the following weekend - June 23/24

i am interested, time permitting - dan

==Monday June 18==
===Soccer at 7:00===
On the field by the gym. Please bring a white and a dark shirt.

==Tuesday June 19==
===Ultimate at 6:30===
Beginners welcome. Please bring a white and a dark shirt.

--
==
--

--'''Basketball'''--
St John's students are challenging us to a game of basketball starting at 6 30 @ the gym. All welcome.
--------------

==Wednesday, June 20==
===Music on the Hill===
Join us for "Music on the Hill" at St. Johns college from 6-8pm for food and drink; this Wed is "Ali Ryerson & The John Trentacosta Quintet". For more info see, [http://www.stjohnscollege.edu/asp/main.aspx?page=6981 schedule here].

===Soccer at 7:00===
Due to the concert, we'll be playing on the far fields. Left out the front entrance, left again, and look for the fields on your right. Should be a short walk from St. John's.

==Thursday, June 21==
===Birthday!===
The 50th birthday ( Golden JUBILEE _!!! ) of one of the CSSS'ers is falling on this date. Guess who ?
Any ideas about a birthday cake, etc ?
: How about we celebrate at "Cowgirls" w/ a cake, music, food and drink. --[[User:Luciano Oviedo|Luciano Oviedo]] 21:57, 10 June 2007 (MDT)
Let us celebrate it as Cultural Night in the Great Hall ( songs, etc from various parts of the world ) !

===Ultimate at 6:30===
Frisbee on the soccer fields.

== Saturday, June 23==
[http://rodeodesantafe.org/ santa fe rodeo], 7pm

* note: this event is now fully booked.

==june 23/24 - Overnight Hike==

Andrew - not sure where to go yet, but it would be fun.

I have a one man tent, would be willing to purchase a 2-man tent if there were others interested in heading out.

I don't think I can go that weekend, but I have a tent that'll fit two people comfortably that I'm happy to lend to anyone who wants to go. [[http://www.santafe.edu/events/workshops/index.php/James_Battin James]]

yeah I could be keen - I haven't got any gear though (aside from boots, pack and water-resistant jacket). will talk turkey during week, dan

perhaps we could find a place to rent tents for the night? -mike

Very likely interested. Plans for a location? Have tent, sleeping bag, boots, car. I have a book of day hikes, but no good topographic maps for overnight camping. -Ben

I have good (35,000:1) topo maps of santa fe/los alamos area & mountain sports (i think this is the right name) in town rents tents (but not s-bags). how about we round table this say mon 17th/tues 18th?? [dan]

==Wednesday, June 27==
* Join us for "Music on the Hill" at St. Johns college from 6-8pm for food and drink; this Wed is Blues, Soul and R&B by "Cathy McGill & Avatar". For more info see, [http://www.stjohnscollege.edu/asp/main.aspx?page=6981 schedule here].

== cricket anyone? ==
I've been getting some sniffs of interest in the game! I can probably arrange a bat here and we can play tennis ball cricket (I can also offer a tutorial on cricket ;) - for proper leather ball cricket, folks are welcome to practice with the UNM cricket club at Albuquerque coming saturday around noon! (dont worry, it's fun cricket and not professional quality either!), the club (and I) then travel to Colorado for a couple of matches 16/17 June; so if some are interested in a Colorado trip, let me know. [[http://www.santafe.edu/events/workshops/index.php/Amitabh_Trehan amitabh]]

Sun, June 10: We had a nice little cricket session at the St. Johns ground today. What about onother one tomorrrow (Mon, Jun 11) sometime. I have some equipment here - bat, pads, stumps, cricket ball and also tennis balls. [[Amitabh Trehan]]
[[Image:Cricket.jpg]]

== Photographers unite! ==
I have met quite a few avid photography enthusiasts here. Let's form a group. NM is a wonderful state for photography, maybe we can plan something! [[http://www.santafe.edu/events/workshops/index.php/Amitabh_Trehan amitabh]]

I'd be happy to point you to some excellent places- we have no shortage here in NM. Lolly lollyb@santafe.edu

I would love to join. The only problem is that I left my camera back home ! HELP ! Saleha Habibullah

Hey, that would be great Lolly !! I'd love to go see some beautiful places ! I'll be writing to you soon :) -- [http://www.santafe.edu/events/workshops/index.php/Amelie_Veron Amelie]

I'm not much of a photographer yet, but I brought my camera, and I’m always looking for opportunities to practice. -- [http://www.santafe.edu/events/workshops/index.php/Jose_Delgado jd]

== El Farol and Other Places to Eat ==
Since the [http://www.elfarolsf.com El Farol Restaurant and Bar] has become immortalized in the complexity literature ([http://en.wikipedia.org/wiki/El_Farol_Bar_problem The El Farol Bar Problem]), we should check it out.

BTW, some locals said the El Farol is a tapas bar and not a full restaurant. See below for more places.

How about an outing some evening next week? Thursday or Friday night (14th or 15th)? I'm staying about a block from El Farol, on Acequia Madre... Should we run the NetLogo simulation first? :) [http://www.santafe.edu/events/workshops/index.php/Mollie_Poynton Mollie].

Some locals told me about a few more great places to eat in town: [http://local.yahoo.com/details?id=20215762 Horseman's Haven] and [http://bobcatbite.com/ Bobcat Bite]. I've also tried The [http://local.yahoo.com/details;_ylt=AiKEjhWdFcvv3xBCmycTIouHNcIF?id=20206492&stx=santa+fe+baking Santa Fe Baking Co] and it was great.

For fine dining [http://www.geronimorestaurant.com/home2.html Geronimo] comes highly recommended.

== mountain biking ==
the dale ball trails starting from the back of st john's provide 22mi+ of what looks like pretty nice trails for biking (& walking!), plus there are many more excellent trails local [http://forums.mtbr.com/forumdisplay.php?s=2e6c56b6542d2b67e39037cc578ead2e&f=91 and otherwise], and there is also a local bus for $2/day to access some of these. I know aussie simon has aquired a trusty steed and I also have a bike arriving so drop me a line if you keen to get amongst it - it is also possible to rent bikes in town, cheers, [http://www.santafe.edu/events/workshops/index.php/Daniel_lester aussie dan]

- yeeeeah. mike - talk to smino re: stealing a bike form him - dan

ok, my bike has turned up (finally) so am keen to have a hack at dale ball trails fri (15th) morn before breeky after losing my lungs and almost my dinner tonight. anyone keen to join? simon, can i borrow your 15mm spanner, I only trust finger-tightened pedals so much... dan

== Anybody sticking around after the CSSS is over ?==
I (Amelie) plan to stay in the region (NM, Colorado, ..) for a week or so after the school. The best would be to rent a car and visit with somebody from the school .. let me know if you're interested :) --[http://www.santafe.edu/events/workshops/index.php/Amelie_veron Amelie]

==Grand Canyon?==
Is anyone else considering visiting the Grand Canyon after CSSS? 
Flagstaff, AZ is about 5 hours away, which is a good place to spend the night with GC a relatively short drive away.
If other people are interested I could drive the long way home to Tucson passing by Flagstaff and spend a couple of days. 
I was there a couple of years ago, but I didn’t have my camera with me then. I would like to fix that stupid mistake. 
In any case, email me if interested. [http://www.santafe.edu/events/workshops/index.php/Jose_Delgado jd]

-----

=Moved done stuff to bottom=
==Monday June 4th==
* at 7pm: soccer match @ the athletic field; be there! [[http://www.santafe.edu/events/workshops/index.php/Olaf_Bochmann Olaf]]

* Monday June 4th, 9pm, Polyhmynia 13, Scotch tasting, hosted by Ben Mazzotta

==Wednesday, June 6th==
* 7pm: climbing @ the [http://www.climbsantafe.com/ Santa Fe Climbing Center]; let's meet at the pond in front of the student centre [[http://www.santafe.edu/events/workshops/index.php/Gregor_Obernosterer Gregor]]

==Friday, June 8th==
* 2pm: Excursion to Taos. [[http://www.santafe.edu/events/workshops/index.php/Gregor_Obernosterer Gregor]] and [[http://www.santafe.edu/events/workshops/index.php/Tim_Johann T1M]]

--I was up that way today. Took the high road and stopped at Chimayo - I thought the Sanctuaria de Chimayo was very, very cool. It is open 9A-6P each day. A little restaurant next door called Oleana's (sp?) serves up homemade tamales until 5P, Thurs-Mon. --Mollie

==Saturday, June 9th==
* some time in the morning: Excursion to southern NM - Socorro and/or White Sands and/or Roswell. [[http://www.santafe.edu/events/workshops/index.php/Gregor_Obernosterer Gregor]] and [[http://www.santafe.edu/events/workshops/index.php/Tim_Johann T1M]]

* Climbing excursion: If you're in, contact me at vikas.shah (at) vanderbilt.edu so we can make plans. We'll be at [[http://www.geocities.com/Yosemite/Trails/9507/lasconchas.htm Las Conchas]] or [[http://www.cs.unm.edu/~moret/crag.html Palomas]]. Let me know which you prefer. I've been to Conchas, fun smaller area with an easy approach. Never been to Palomas, has a substantially longer approach. I have topos available for both; descriptions and some of the routes are described at the links above. [[http://www.santafe.edu/events/workshops/index.php/Vikas_Shah Vikas Shah]]
**''Update 6/7 1:30PM :'' My car is full. If anyone else would like to come, we'll have to arrange for another driver to come.
**''Update 6/8 8:50AM :'' There was unfortunately an injury, and one of the people going had to back out. There's room for one more.

==Hike to Nambé Lake, Saturday, June 9th==
Folks: we will hike to Nambé Lake, which is a less-strenuous hike in the same area as Santa Fe Baldy. The guide book says the lake is a “special treat”, and there are apparently lots of wildflowers. It is a 5-hour trip (including lunch stop), 7 miles return. The plan is to meet at 9.30am in the usual spot (same place from where the shuttle buses take us to SFI).

The first ten confirmed people are: me (Ryan), Simon, Mike, Elise, Monika, John, Dan, James, Hannah, Fred…

Please add yourself to this list if you want to come (apologies if you gave me a verbal commitment and I forgot).

John has kindly offered to drive and we will also be renting one car. If you want to come and aren't on the list above, please figure out your own transport arrangements (I think Michigan Will might be driving too).

Please bring: lunch (we can stop at a store in the morning); water (2 litres); a raincoat; a warm jumper; decent footwear; sun protection.

== Sunday, June 10: Join me for Church, 11am ==
I'm planning to go to visit a nearbye [http://www.calvarybaptistsantafe.com Baptist church], all are welcome to come. I will likely ride there. I can arrange another bike, or if we are many, perhaps a car. Please let me know below, or by email if you'd prefer. If you wanted to join me for Bible study on a one-off or weekly basis (this would be sitting round to read a passage of the Bible and discuss it) then let me know (again, by email if you'd prefer). All persuassions and questions welcome! [[Simon_Angus]] (s.angus AT unsw.edu.au)

I'm interested in both, but don't have a bike or car to get to church... how far is it? Heather (hbeil AT email.unc.edu)

==Sunday, June 10 - Hike up Atalaya==
Anyone up for a hike this afternoon? I know a bunch of you are probably hiked out after yesterday's excursion, but if anyone would like to tackle Atalaya this afternoon, there is a group of us leaving around 3pm. We'll meet on the road by the dorms at the top of the hill at 3. Hope to see some of you there! ->Josh

Agent-Based Modeling: Non-Technical Overview and Applications

2007-06-14T02:57:12Z

Natasha:

===Summary===

This page continues the original posting [[Non-Technical Introduction and Overview]]. I originally posted this on the Tutorial Requests section of the [[CSSS 2007 Santa Fe-Tutorials]] page. I'm happy to present something during week two. Please post some recommended times and if there are any specific questions about agent-based modeling that people want me to try and address.

[[Aaron Frank]]

=== Participants ===
* I'm interested. Not sure about times. Mike
* [[Brian Lawler]] is interested
* Me too!!! Natasha

Cellular Slime Mold Simulation

2007-06-11T05:30:36Z

Natasha: /* Who's interested? */

{{CSSS 2007 Santa Fe}}
= News =
I'm really happy that there has been some interest in this project. Besides the people on the list below, a few other persons have also reported interest in maybe joining the project. To allow for as many people as possible to join, I propose that we have our first meeting on monday the 11th. Shall we say after dinner, at 6 pm? "Homework" till then will be to read the article ([http://homepages.ed.ac.uk/nsavill/Papers/dicty.pdf]) and think a little of what we want to get out of the project. /Johan

= Background =
One of the most widely studied and relatively simple organisms in which to study morphogenesis (the shapes of organisms and the positions in the organisms of various specialized cell types) is the so-called cellular slime mold. It provides a simple model organism for studying many general developmental processes, including chemotaxis (behavioral response by an organism to a directional chemical stimulus), cell sorting, pattern formation and complex behavior through self-organization.

Normally, slime mold is a unicellular amoeba, but when food resources become scarce, they aggregate and form multicellular organisms that can move towards food sources.

= Proposition =
There is an article by N. J. Savill and P. Hogeweg ([http://homepages.ed.ac.uk/nsavill/Papers/dicty.pdf]) where a model of the morphogenesis of these slime mold organisms is presented. What amazes me with this article is that the model seems to be relatively simple, but that it can still account for the whole morphogenetic process from single cells to a larger aggregate of cells, and finally to a multicellular organism capable of coordinated motion.

I propose a project group for implementing this model and possibly extend it in directions that we find suitable. I’m sure some very interesting questions will pop up along the way.

= More about the model =
The simulations are based on a cellular automata (CA) model, where each amoeba is represented as a collection of CA cells. A Monte Carlo simulation is performed, where amoebae of different types have a tendency to group together. This results in a cell sorting behavior. Another mechanism in the model is communication between amoebae via cAMP (cyclic adenosine monophosphate) chemicals, modelled by a partial differential equation. This results in aggregation of the amoebae into a ”multicellular organism” (interesting philosophical/biological question if this really counts as a multicellular organism). Without any change of parameters, the slime mold eventually starts to move guided by cAMP waves. The whole process seems to very much resemble what happens for living slime mold.

= So, what coworkers am I looking for... =
Well, anyone interested in Cellular Automata models, Partial Differential Equations, Monte Carlo simulations, cell biology, evolution etc. People interested in computer graphics are also very welcome so that we get some cool movies to show in the end :-). I would very much appreciate participation from someone with more biological knowledge than myself (which is not a lot). I’m sure there are some interesting questions here concerning formation of multicellular organisms in general that could serve as a good discussion within this work.

= Who's interested? =
* Johan Nyström (nystjoha@chalmers.se)
* Will Ludington
* Tim Johann
* Ryan Chisholm
* Dan Lester - maybe before we get together on monday, have a think about scope for this project, especially something of biological importance
* Natasha - I would like to know the date and time of meeting.

Artificial Neural Networks

2007-06-11T04:39:03Z

Natasha:

Willing to offer an introduction to ANNs if anyone is interested! [[Mollie Poynton]]

Just add your name below...

Yes, I'd love it. Vikas

very interested. --jd

same here. Amir

I would like to attend. Saleha

I would do anything to learn how to build an attractor neural network. -Mike

''Hey - that's an interesting statement :) Unfortunately, I can't help with attractor neural nets. - MP

Count me in. --James

interested - Nate

I'm interested. - Brian

Ya i would like to know also. --> Natasha

Closure Under Inversion

2007-06-11T04:36:51Z

Natasha:

I would be happy to give a tutorial on the newly developed class of probability distributions that are Strictly Closed Under Inversion. By presenting this work in front of people as bright and intelligent as yourselves, I hope to get some clues regarding the true Significance of this concept in Real - Life situations.

Saleha Habibullah

Hi Saleha, I'd be happy to hear about your new classes of probability distributions ! You'll have to count on my [very] rusty statistical knowledge though .. but I'm definitely interested. -- [[User:Amelie|Amelie]] 00:53, 5 June 2007 (MDT)

Count me in. [[User:KristenF|KristenF]]

Great ! ( Saleha )

i'm in. rafal

me too. James

I am interested. Amitabh

I am also coming. --> Natasha

Let us have it on Wednesday, 13 June from 7 to 8 pm. Will that be OK for everyone ? ( Saleha )

Cellular Automata

2007-06-11T04:34:22Z

Natasha: /* Sign in below */

Back to [[CSSS_2007_Santa_Fe-Tutorials]]

== Overview ==

A tutorial on Cellular Automata (CAs) was a requested tutorial (not sure by whom).

It doesn't look like CAs will be covered in any of the modules, so I'm happy to do a tutorial on them. I will check this with Dan before scheduling.

Am currently thinking of the following format:
# Micro-mechanics of CAs (how they work)
# Example tools to run them
# Looking at several interesting CAs
# Emergent structure in CAs
# Computation in CAs

Please add requests if I've missed an important topic. Happy to co-facilitate if anyone else is interested in doing so. In any case, I think it would be best run informally, so you can add your expertise without formally facilitating.

As a follow-up, I'll put up a suggested tutorial on my work on local information dynamics (i.e. computation) in complex systems, for which CAs are used as example complex systems.

[[Joseph_Lizier]]

== Sign in below ==

Add your name if you are interested.

[[User:Amirig|Amir]]
 
jd 
[[User:KristenF|KristenF]]
 
Will L 
[[Alex Healing]]

Frederic 
[[Aaron Frank]]
 
Nathan Menke

Natasha

== Schedule ==

Cool, that looks like critical mass.

I'm going to suggest Wednesday June 13, 9 am. I'll add it to the schedule. Complain below if that's not good and if there are a few it's not good for we'll see if we can move it.

Consciousness and/or visual processing

2007-06-11T04:33:06Z

Natasha:

{{CSSS 2007 Santa Fe}}

Hi, I'd be happy to do a tutorial on the current state of knowledge about consciousness or visual processing if people are interested. Perhaps add your name here or I will start a post on the forum to sense interest. Vikas

I'm very interested! Kai

Sounds like a great topic. /Johan

I would like to attend. Saleha Habibullah

I am especially interested in the consciousness tutorial. /Mike Wojnowicz

Count me in. --[[User:Luciano Oviedo|Luciano Oviedo]] 23:23, 4 June 2007 (MDT)

Count me in too ! -- [[User:Amelie|Amelie]] 00:49, 5 June 2007 (MDT)

I'd be interested to know more about consciousness :o) Hannah

Interested. --[[Jose Delgado]]

Very interested. -- Risi.

Count me in - Kath

I am comin' - Amitabh

I'm in. [[User:KristenF|KristenF]]

Sounds interesting. -->Natasha

Eigenvectors and Eigenvalues

2007-06-11T04:29:58Z

Natasha:

given demand, I am happy to give a brief overview/dicussion on what are linear eigenspaces (or e-vectors and e-values) in light of how they crop up in nonlinear dynamics and how they relate to behaviour around hyperbolic points - i.e. liz bradley's "horse diagram" elucidated. no background math necessary (ok, a little linear algebra and basic differential calculus might be handy, but we won't be touching homoclinic tangles etc...). post below if u keen and we can setup a short session,

cheers dan

*I am DEFINITELY interested ! Saleha Habibullah
*Im also interested dan! Frederic Bartumeus
*Sweet. Vikas
* I'm in! Rhonda
* yeah, I could use a refresher! -> Josh
* i'm in. rafal
* I'm interested. - Brian
* yeah that would be great. -Will L.
* I'm in. --jd
* Count me in. -Kristen
* Sounds interesting. When will it be? Mike
* Will B.
* Count me also. -->Natasha

ok, it seems there is plenty of interest - I will organise a session from 10:30am-11:30am on Wednesday June 13 at 2nd Floor Senior Seminar Room - post below if that does not suit - dan

Any chance of having it sometime Wednesday morning?

Ok, !!NOTE NEW TIME!! 10:30am-11:30am on Wednesday June 13 at 2nd Floor Senior Seminar Room

Matlab tutorial

2007-06-11T04:27:53Z

Natasha:

{{CSSS 2007 Santa Fe}}

Basic Matlab programming for anyone who's interested + running a few
example simulations (fractals, logistic map and maybe more…)
Please let me know (yael.artzy@gmail.com).
Thanks ,Yael

'''''Update 1:'''''

Unfortunately I couldn't find an empty slot for the tutorial this week, so I wrote it down for next Monday after dinner. If any one can think of an earlier time, or if you prefer a different time, that would be fine with me.

A few words about what I am planing:

I will first be going over some very basic stuff (getting Matlab started, basic commands and functions, m-files,...). After that I'd like to demonstrate how to code and run a few simple programs (based on examples seen in the lectures), and if we still have time... well, I'll have some more stuff ready.

See you,

Yael

'''''Update 2:'''''

Because there might be a problem getting every who's interested in the
tutorial free at the same time, I suggest posting alternative
times&dates on Wiki (see below). Please write down your name next to the time that's good for you (you can write your name in more than one option).
This way we can get a feeling of when the best time would be. If this
proves to be too complicated, I can always do it twice.

Yael

PS- if there are any special requests or proposals, feel free to tell me.

'''''Setting a time:'''''

Opt #1: Monday after dinner (Kai, rafal, Saleha, Amir, Heather, Natasha)

Opt #2: Wednesday morning 10:30-11:30 (Vikas, Rhonda, jd)

Either: Brian, Ben, James

I'm in for this. Vikas

Ditto. Aaron

I am also in. --jd

Me too ! Saleha

count me in. rafal

Me too. --James

Me too--Rhonda

Me too. Brian

Yesh. --Will B.

Me too. Sayan

Friday 1:00 Lab Signup

2007-06-08T04:40:20Z

Natasha:

# rafal raciborski
# Amelie Veron
# Johan Nystrom
# Simon Angus
# Luis Pinzon
# Alejandro Balbin
# Aaron Frank
# Olaf Bochmann
# Will Ludington
# Monika Piotrowska
# john mahoney
#Natasha Qaisar

Natasha Qaisar

2007-04-03T19:40:34Z

Natasha:

Hello Everyone!
I'm Biotechnologist (B.Sc Hons) and currently lecturer at Centre of Biotechnology, University of Peshawar,Pakistan.I teach genomics, bioinformatics & bioethics.My previous research work was to find out the ligand binding site & key interactions of the enzyme ''aldehyde dehydorgenase'' with its confactor by using structural bioinformatics.My main research interest is the holistic concept of systems biology,and the leading-edge technologies of genomics, proteomics and bioinformtaics.
As today we need to understand function not on a individual gene/ protein level but on multimolecular modules and even more complex systems, my reserach interest is to gain newer insights into the pathogenesis of third-world countries infectious diseases and cancer, and development of new drugs & therapeutics by the application of systems biology.I think the emergence of systems biology has resulted in better understanding of disease mechanism because it explains how the molecular charactersitics of cellular components give rise to the complex organization and integrated properties of a cell, tissue, organ, or organism as a whole.

Hoping to meet you all at CSSS this summer.

Natasha Qaisar Khan
Centre of Biotechnology
University of Peshawar
Peshawar,Pakistan.
Email: khanatasha@gmail.com

Natasha Qaisar

2007-03-31T18:41:27Z

Natasha: