From tragopan at sonic.net Tue Oct 16 15:01:30 2007 From: tragopan at sonic.net (Mark Halverson) Date: Tue, 16 Oct 2007 15:01:30 -0700 Subject: [Santa-rosa-pm] Active? Message-ID: <471534BA.7080505@sonic.net> Is this mailing list active? I haven't seen any posts....I am looking to learn perl - I have no programming experience - and learn best in a lab or one-on-one (I have tried the books). -Mark From george at metaart.org Tue Oct 16 16:13:02 2007 From: george at metaart.org (George Woolley) Date: Tue, 16 Oct 2007 16:13:02 -0700 Subject: [Santa-rosa-pm] Active? In-Reply-To: <471534BA.7080505@sonic.net> References: <471534BA.7080505@sonic.net> Message-ID: <200710161613.02694.george@metaart.org> hi mark, george here, coordinator of the oakland.pm group. thanks for your communication and thanks for your interest in perl. as far as i know the list is active, but there are usually only a few posts. i expect there will be a post about the october meeting later this month; i understand the group meets the last tuesday of most months. do you have a request re learning perl? - george On Tuesday 16 October 2007 15:01, Mark Halverson wrote: > Is this mailing list active? > > I haven't seen any posts....I am looking to learn perl - I have no > programming experience - and learn best in a lab or one-on-one (I have > tried the books). > > -Mark > > > _______________________________________________ > Santa-rosa-pm mailing list > Santa-rosa-pm at pm.org > http://mail.pm.org/mailman/listinfo/santa-rosa-pm From bob at ted.net Tue Oct 16 16:17:11 2007 From: bob at ted.net (Bob Blick) Date: Tue, 16 Oct 2007 16:17:11 -0700 (PDT) Subject: [Santa-rosa-pm] Active? In-Reply-To: <471534BA.7080505@sonic.net> References: <471534BA.7080505@sonic.net> Message-ID: On Tue, 16 Oct 2007, Mark Halverson wrote: > Is this mailing list active? Yes, it's just not very busy most of the time. > I haven't seen any posts....I am looking to learn perl - I have no > programming experience - and learn best in a lab or one-on-one (I have > tried the books). I've always learned things when I had a specific task I needed to do. I also like the book "Perl Cookbook". You should come to a meeting and see what you think. It's a great bunch of people. And there's usually some perl going on. Cheerful regards, Bob From orsini at sonic.net Tue Oct 16 16:20:37 2007 From: orsini at sonic.net (Rob Orsini) Date: Tue, 16 Oct 2007 16:20:37 -0700 Subject: [Santa-rosa-pm] Active? In-Reply-To: <471534BA.7080505@sonic.net> References: <471534BA.7080505@sonic.net> Message-ID: <05CDAF52-6BDD-4D25-8D21-94AE637D2CB8@sonic.net> On Oct 16, 2007, at 3:01 PM, Mark Halverson wrote: > I haven't seen any posts....I am looking to learn perl - I have no > programming experience - and learn best in a lab or one-on-one (I have > tried the books). What about a JC course? If you really have no programming experience, you might look into Python or Ruby instead of Perl. (Am I allowed to say that here? :) Their syntax is a little less of a barrier to entry, IMO. Rob From geverscott at foothill.edu Tue Oct 16 16:56:49 2007 From: geverscott at foothill.edu (Scott Gever) Date: Tue, 16 Oct 2007 16:56:49 -0700 Subject: [Santa-rosa-pm] Active? In-Reply-To: <471534BA.7080505@sonic.net> References: <471534BA.7080505@sonic.net> Message-ID: <47154FC1.1040601@foothill.edu> Hi Mark, et al., I've been teaching Perl programming at Foothill College (Los Altos Hills) for a number of years. This quarter is my first time presenting the class strictly over the web and internet, which means that it's accessible from almost anywhere. For the moment, it sounds like you're not ready for it but you might want to keep it in mind if you're not in great hurry. The course has a softer flavor of prerequisites, that we call advisories so that a student may prepare for the course with equivalent experience as opposed to institutional based(i.e. the exact class specified or counselor based approval) experience. Essentially, the course I teach "advises" that the student have the equivalent of an introductory programming class using any of C, C++, or Java, AND an introductory class in Linux/Unix. Lastly, the online format isn't for everyone (maybe not even me!) because there's very little opportunity to skim and slide; involvement and serious commitment are co-requisites. So, if you or anyone else are interested, feel free to have a look around my class web site to get an idea of what's going on and also feel free to contact me for further info or advice. Cheers, Scott Gever p.s. I'm getting a new Perl programming course ready for Spring quarter based entirely on O'Reilly's Intermediate Perl book. ;) p.p.s. my full time work is system Administration at that other search engine group in Mountain View . 8-) Mark Halverson wrote: > Is this mailing list active? > > I haven't seen any posts....I am looking to learn perl - I have no > programming experience - and learn best in a lab or one-on-one (I have > tried the books). > > -Mark > > > _______________________________________________ > Santa-rosa-pm mailing list > Santa-rosa-pm at pm.org > http://mail.pm.org/mailman/listinfo/santa-rosa-pm > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.pm.org/pipermail/santa-rosa-pm/attachments/20071016/f2c198f8/attachment.html From bob at ted.net Tue Oct 16 16:58:39 2007 From: bob at ted.net (Bob Blick) Date: Tue, 16 Oct 2007 16:58:39 -0700 (PDT) Subject: [Santa-rosa-pm] Active? In-Reply-To: <05CDAF52-6BDD-4D25-8D21-94AE637D2CB8@sonic.net> References: <471534BA.7080505@sonic.net> <05CDAF52-6BDD-4D25-8D21-94AE637D2CB8@sonic.net> Message-ID: On Tue, 16 Oct 2007, Rob Orsini wrote: > What about a JC course? If you really have no programming experience, > you might look into Python or Ruby instead of Perl. (Am I allowed to > say that here? :) Hi Rob, Only if you back it up with something factual and/or witty, like this webcomic: http://www.xkcd.com/312/ Cheerful regards, Bob From geoff at broadwell.org Tue Oct 16 20:20:16 2007 From: geoff at broadwell.org (Geoffrey Broadwell) Date: Tue, 16 Oct 2007 20:20:16 -0700 Subject: [Santa-rosa-pm] Active? In-Reply-To: References: <471534BA.7080505@sonic.net> <05CDAF52-6BDD-4D25-8D21-94AE637D2CB8@sonic.net> Message-ID: <1192591216.8228.206.camel@beast.home.broadwell.org> On Tue, 2007-10-16 at 16:58 -0700, Bob Blick wrote: > On Tue, 16 Oct 2007, Rob Orsini wrote: > > What about a JC course? If you really have no programming experience, > > you might look into Python or Ruby instead of Perl. (Am I allowed to > > say that here? :) > > Hi Rob, > > Only if you back it up with something factual and/or witty, like this > webcomic: > > http://www.xkcd.com/312/ And then of course there's: http://xkcd.com/297/ http://xkcd.com/224/ http://xkcd.com/208/ xkcd rules. -'f From orsini at sonic.net Tue Oct 16 20:29:41 2007 From: orsini at sonic.net (Rob Orsini) Date: Tue, 16 Oct 2007 20:29:41 -0700 Subject: [Santa-rosa-pm] Active? In-Reply-To: <1192591216.8228.206.camel@beast.home.broadwell.org> References: <471534BA.7080505@sonic.net> <05CDAF52-6BDD-4D25-8D21-94AE637D2CB8@sonic.net> <1192591216.8228.206.camel@beast.home.broadwell.org> Message-ID: On Oct 16, 2007, at 8:20 PM, Geoffrey Broadwell wrote: > On Tue, 2007-10-16 at 16:58 -0700, Bob Blick wrote: >> On Tue, 16 Oct 2007, Rob Orsini wrote: >>> What about a JC course? If you really have no programming >>> experience, >>> you might look into Python or Ruby instead of Perl. (Am I allowed to >>> say that here? :) >> >> Hi Rob, >> >> Only if you back it up with something factual and/or witty, like this >> webcomic: >> >> http://www.xkcd.com/312/ > > And then of course there's: > > http://xkcd.com/297/ > http://xkcd.com/224/ > http://xkcd.com/208/ > > xkcd rules. This isn't related to the comics, and it's still not related to Perl (except in an ancestral sort of way)... but it's cool, none the less: http://hacketyhack.net/ That'll teach you some programmin'!! It's actually a very cool project. Everyone should have a look. If you really want to learn Perl, bring some hot dogs to our next meeting and I'll teach you, one-on-one, the basics (just the basics) of this dark and illusive language you've heard so much about. When's the next meeting? Rob -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.pm.org/pipermail/santa-rosa-pm/attachments/20071016/e7cf6df0/attachment-0001.html From rjw at alembic.com Mon Oct 22 00:23:41 2007 From: rjw at alembic.com (Ron Wickersham) Date: Mon, 22 Oct 2007 00:23:41 -0700 (PDT) Subject: [Santa-rosa-pm] October Meeting Message-ID: the next meeting is Tuesday night, 30 Sep 2007 19:30. our meeting place is Alembic, 3005 Wiljan Ct., Santa Rosa. directions are at http://sonoma.pm.org/directions.html -ron /~\ The ASCII Ribbon Campaign \ / No HTML/RTF in email X No Word docs in email / \ Respect for open standards From geoff at broadwell.org Mon Oct 22 09:53:51 2007 From: geoff at broadwell.org (Geoffrey Broadwell) Date: Mon, 22 Oct 2007 09:53:51 -0700 Subject: [Santa-rosa-pm] October Meeting In-Reply-To: References: Message-ID: <1193072031.8228.233.camel@beast.home.broadwell.org> On Mon, 2007-10-22 at 00:23 -0700, Ron Wickersham wrote: > the next meeting is Tuesday night, 30 Sep 2007 19:30. First, that says "Sep" above ... but second, shouldn't it be *next* week? -'f From rjw at alembic.com Mon Oct 22 11:04:06 2007 From: rjw at alembic.com (Ron Wickersham) Date: Mon, 22 Oct 2007 11:04:06 -0700 (PDT) Subject: [Santa-rosa-pm] October Meeting In-Reply-To: <1193072031.8228.233.camel@beast.home.broadwell.org> References: <1193072031.8228.233.camel@beast.home.broadwell.org> Message-ID: On Mon, 22 Oct 2007, Geoffrey Broadwell wrote: > On Mon, 2007-10-22 at 00:23 -0700, Ron Wickersham wrote: >> the next meeting is Tuesday night, 30 Sep 2007 19:30. > > First, that says "Sep" above ... but second, shouldn't it be *next* > week? > > > -'f yes, the meeting is next week, on tuesday 30 Oct 2007. -ron From rjw at alembic.com Tue Oct 30 02:39:06 2007 From: rjw at alembic.com (Ron Wickersham) Date: Tue, 30 Oct 2007 01:39:06 -0800 (PST) Subject: [Santa-rosa-pm] October Meeting Message-ID: the next meeting is tonight, Tuesday night, 30 Oct 2007 19:30. our meeting place is Alembic, 3005 Wiljan Ct., Santa Rosa. directions are at http://sonoma.pm.org/directions.html -ron /~\ The ASCII Ribbon Campaign \ / No HTML/RTF in email X No Word docs in email / \ Respect for open standards From wgheath at gmail.com Wed Oct 31 12:19:03 2007 From: wgheath at gmail.com (William Heath) Date: Wed, 31 Oct 2007 12:19:03 -0700 Subject: [Santa-rosa-pm] Modeling synthetic biological software approaches questions/analysis Message-ID: Hi All, I went to a perl programming meeting last night and discussed approaches to both creating a simulator of cells working via software and also how dna/cells really are software/computational instruments. I hope this is not too technical for everyone but I am going to attempt to describe the approach that nature has taken with the programming of DNA to do work: 1. Nature has chosen DNA as the "programming language/software" for doing work I then specified a simple example of a requirement to create a piece of DNA software to construct a bottle cap made of cells starting with one cell. When working with software in computers you can call functions/libraries. The functions that allow you to do work with DNA are as follows: 1. Activating genes via promoter regions 2. De-activating genes via promoter regions 3. Changing the cell membranes receptors via genes to allow/disallow chemicals/proteins to get into the cell 4. Producing a salinity differential inside a cell to cause osmosis to occur allowing chemicals to get in or out of the cell 5. Changing the electrical differential to cause chemical movement in/out of the cell 6. Causing the cell to divide (Do we know how to tell a cell to divide yet?) 7. Telling a cell to die 8. Using RNAi to disallow previously allowable genes from turning on 9. Building proteins that within a cell will go to a certain organelle 10. Using chemical signals to cause cells to do things 11. Using the theory of chemical diffusion to send messages/get messages to cells 12. Attaching a protein to a motor protein to cause exocytosis to occur 13. Causing a cell to differentiate into a different kind of cell by chemical signals, the texture with which the cell is in contact (physically) 14. Generate ATP from mitochondria for energy (Do we know how to tell mitochondria how much to make etc... yet? I still don't understand how glycogen gets into the cell for the mitochondria to convert to ATP or even specifically how ATP is used to make the cell do anything etc...) 15. Detection of what cells are around a cell to cause the cell to do things (I know that some cells will only grow a first layer and after they detect that this first layer is created that they stop dividing) 16. Influencing of free energy to bias/control the way a protein folds which in turn causes other side effects such as what proteins can even get into a cell etc... 17. Secrete waste via endoplasmic reticulum (Do we know how to tell a cell to do this in a controlled way or is it automatic? Another question is what is automatic in a cell that a software developer of DNA can take for granted? For example, an operating system has automatic functionality etc...) Can anyone else think of any other functions that can be invoked via DNA that I missed? I didn't cover viruses as a tool for doing work with cells but I guess that is a possibility. Now I want to ask you a question that is probably too hard to answer but if anyone has courage to try, use the functions I have specified in 1 - 17 to construct a bottle cap starting with one cell that you inject your dna software into. \_/ <- bottle cap I will show you my attempt at creating a 3 dimensional bottle cap: I am assuming the cell is in a uterus of some kind initially. My DNA program runs as follows: 1. Tell my initial cell to divide (Using functions: 1, 2, 6) 2. Somehow tell the 2 cells to join together in a plane (making the top of the cap, don't know what function could cause this, anyone know?) 3. Repeat steps 1 through 2 until the top of the cap is created (using function 15 to know to stop all cells dividing) 4. Using diffusion signal the outer cells to begin to divide upward (Using functions: 11, 1, 2, 5. Note that the cells dividing upward are at least 2 deep, I will tell you why in a minute) 6. Repeat steps 5 through 6 until the sides of the cap are created (using function 15 to know to stop all cells dividing) 7. Signal the inner cells that are in a spiral patten to die forming the cork screw type structure of the cap to twist onto the top of the bottle (Using functions: 1, 2, 7, 11) What would be even more amazing if someone could help me match my functions 1 - 17 to real biobrick functions! Anyway, please let me know your opinions on my analysis/appraoch. I also asked at my perl programming group what they felt was the best language to model/simulate a cell working. They thought it was prolog as a cell basically is composed of a system of constraints. What do you all think? -Tim From mcglk at artlogix.net Wed Oct 31 14:10:00 2007 From: mcglk at artlogix.net (Ken McGlothlen) Date: 31 Oct 2007 13:10:00 -0800 Subject: [Santa-rosa-pm] Modeling synthetic biological software approaches Message-ID: <86odefous7.fsf@c3po.artlogix.com> Hi, Tim (or William). It sounds like you're working on a fascinating project. I don't really have that much to add, per se, to the biological modeling, as you're in well over my understanding of DNA operands. :) However . . . | I also asked at my perl programming group what they felt was the best | language to model/simulate a cell working. They thought it was prolog as a | cell basically is composed of a system of constraints. What do you all | think? Welllllll, Prolog would work. I've used Prolog, and I liked using it---and yes, you could probably hammer out a program in it that would simulate this. I'm not sure that Prolog is the best language for it, though. While this might be a biased statement based on my nascent enthusiasm for the language, I would probably still recommend looking into Haskell. http://haskell.org/haskellwiki/Introduction Like Prolog, Haskell allows you to specify what should be computed, without specifying sequence or enforcing a strict order. Haskell itself will work out the dependencies for you, and its syntax (while a bit regular-expressionish at times) will allow you to write the rules of your system relatively concisely. It will also allow you to change the rules a bit more easily than a lot of other languages would (but on a par with Prolog, I think). Do check it out. ---Ken From wgheath at gmail.com Wed Oct 31 14:22:16 2007 From: wgheath at gmail.com (William Heath) Date: Wed, 31 Oct 2007 14:22:16 -0700 Subject: [Santa-rosa-pm] Modeling synthetic biological software approaches In-Reply-To: <86odefous7.fsf@c3po.artlogix.com> References: <86odefous7.fsf@c3po.artlogix.com> Message-ID: Hi All, Regardless of what language we use fundamentally I think we have agreed that this is a constraints based algorithm that should be used to model how cells work. I just talked with a physics phd friend I have and he mentioned that is really a constraint minimization problem. I saw some truth to this in that the cell itself is always trying to minimize differentials between itself and the outside world via endocytosis, osmosis etc... Proteins fold based on minimizing free energy usage. How does that sound to you all? -Tim On 31 Oct 2007 13:10:00 -0800, Ken McGlothlen wrote: > Hi, Tim (or William). > > It sounds like you're working on a fascinating project. I don't really have > that much to add, per se, to the biological modeling, as you're in well over my > understanding of DNA operands. :) However . . . > > | I also asked at my perl programming group what they felt was the best > | language to model/simulate a cell working. They thought it was prolog as a > | cell basically is composed of a system of constraints. What do you all > | think? > > Welllllll, Prolog would work. I've used Prolog, and I liked using it---and > yes, you could probably hammer out a program in it that would simulate this. > > I'm not sure that Prolog is the best language for it, though. While this might > be a biased statement based on my nascent enthusiasm for the language, I would > probably still recommend looking into Haskell. > > http://haskell.org/haskellwiki/Introduction > > Like Prolog, Haskell allows you to specify what should be computed, without > specifying sequence or enforcing a strict order. Haskell itself will work out > the dependencies for you, and its syntax (while a bit regular-expressionish at > times) will allow you to write the rules of your system relatively concisely. > It will also allow you to change the rules a bit more easily than a lot of > other languages would (but on a par with Prolog, I think). > > Do check it out. > > ---Ken > From mcglk at artlogix.net Wed Oct 31 15:04:45 2007 From: mcglk at artlogix.net (Ken McGlothlen) Date: 31 Oct 2007 14:04:45 -0800 Subject: [Santa-rosa-pm] Modeling synthetic biological software approaches Message-ID: <86lk9jx7nm.fsf@c3po.artlogix.com> | Regardless of what language we use fundamentally I think we have agreed that | this is a constraints based algorithm that should be used to model how cells | work. Oh, no, I agree perfectly with that. Life itself is more or less a constraint minimization issue, after all---everything free to work within the limitations of their nature, or adaptation or death must occur. I was also doing some thinking about your bottle-cap-forming cell problem, and another computer language possibility occurred to me: breve. In breve, you define the behaviors of agents in a 3D space, and creating visualizations of those is relatively easy. It should be people to create constraint-based simulations for each object on multiple levels (genomic, cellular, etc.). You can check that out at http://www.spiderland.org/ One nice thing about breve is that it's easier than Haskell, and getting a visual of what's going on is also a lot easier as well. It's open-source, and available for Linux, OS X and Windows. ---Ken