Talk:List of digital organism simulators

Guide For Inclusion
Some sort of minimal standard level is needed to prevent simulators from being listed that only really take up space on the page, and distract readers from more worthwhile simulators.

Here are some ideas for necessary qualities a sim should have to be listed:


 * 1) The organisms should have a DNA program/file/structure that tries to be complex (perhaps even Turing complete). So sims that just have organisms with a few parameters that can mutate aren't sufficiently complex. edit: Neural Net based and parameter simulators are acceptable, but should be in their own, later sections.  --Numsgil 21:30, 5 November 2005 (UTC)
 * 2) The program should be finished. Or mostly finished.  To the point where you can run it and get something out of it for your time. --Numsgil 00:34, 30 May 2006 (UTC)
 * There are plenty of programs that have been in working states for a long period of time but may not be considered "finished" by their authors. What I understand from your striking out the latter part of your comment is that you believe only programs that are no longer being improved upon belong here. Af1218 20:11, 1 May 2007 (UTC)
 * The idea is that programs listed should have most of these qualities. Most simulators are always being updated, but I want to avoid listing unremarkable, unfinished simulators.  JoeSchmoe's program he started programming 3 months ago really shouldn't be listed.  --Numsgil 20:31, 1 May 2007 (UTC)


 * 1) The program should either have been around for a while or be involved in research, or otherwise demonstrate an appeal beyond just its creator. This is rather vague however.
 * 2) The program should have some sort of homepage or presence on the web, even if it's just a wikipedia article. It'd be rather pointless to list a simulator as just a name and not give any place to go find it.
 * 3) *As a sub point, the program should be able to either be able to be bought or (preferably) downloaded from somewhere so people can actually find and use it.

Just some of my thoughts on the matter. --Numsgil 18:15, 22 October 2005 (UTC)

The finish part do i think is not nesseserly, what if the guy/team who makes it needs ideas? dont you think they should be able to put it up so people go there and so they might get help?


 * If it's not finished how do we know it will ever be, or should even be of interest to anyone else? Wikipedia is not (oo, I hate that.  Sounds so strict) an advertising venue.  --Numsgil 19:08, 26 October 2005 (UTC)

I think the first part is too strict in retrospect. It should just be another section of this page. Divide the page into simulators that involve actual programs, those that involve parameters, those that involve neural nets, etc. --Numsgil 19:07, 26 October 2005 (UTC)

I've created a section for neural net based simulators like Creatures. I think for inclusion a population of organisms must be present. That is, something like the game Black and White probably shouldn't go here. --Numsgil 19:21, 26 October 2005 (UTC)

That thing about biological dna, how would anyone use ATCG for a alife DNA? --Zelos
 * You'd have to simulate all (or alot) of organic chemistry. Good luck with that.  --Numsgil 21:30, 5 November 2005 (UTC)

Darwinbots have been removed because the leader of it removed other ones and therefor dont deserve to have his link here
 * Links were removed that failed to meet the criteria for inclusion above. --Numsgil 18:55, 10 November 2005 (UTC)
 * what i know it was you who made it and it havent been a election for it and therefor is not decieded to be in action
 * Please sign your statements Zelos (I've done it just now for you). I forget alot myself, but it's important to remember.  If you have issues, instead of performing an edit war why don't we get a moderator to moderate?  I believe my guidelines for inclusion above are very much in the realm of "right on".  Considering your own page on CELL got deleted from Wikipedia, don't you think perhaps trying to include it in this matter is a bit underhanded and immature?  If you can get CELL an actual page on Wikipedia that isn't deleted (and's been up for a while towards this end) then I'd see no reason not to include it in this listing.  Otherwise, you're just cluttering up the space away from more viable simulators.  --Numsgil 07:05, 11 November 2005 (UTC)
 * Who is zelos?a friend of yours? And if i had a account dont you think i would sign it then?
 * i am zelos. y am i getting the blame for this nums?--Zelos
 * Oh, terribly sorry anonymous poster. Perhaps you should create an account so you can sign your comments.  --Numsgil 03:39, 12 November 2005 (UTC)
 * it is ok. i do not really have a internet name. But i still belive that your list is not in action cause there havent been somekinda election for it.
 * mmm, and you feel that I should be including programs that aren't done yet in the list? --Numsgil 17:20, 12 November 2005 (UTC)
 * Well now it is released, a alpha but it still counts, so im adding it nums, -Zelos
 * I'd feel better if you let it sit for a while and demonstrate merit. Everything else on the list has been around for a while and some have even been used in active research.  As an acid test, write a wiki article on CELL and let it sit for a while.  When you do so and it hasn't been deleted as a vanity page, I'd be much more inclined to add it.   --Numsgil 06:28, 15 November 2005 (UTC)
 * now im getting really pist off nums -Zelos
 * Would you like me to solicit a third opinion? Get someone else to add input?  That's not a problem.  Every other thing in the list are relatively big players with a user base of more than one.  I made it very clear in the criteria for inclusion above (which you can dispute if you like, and we can get some more people to comment on it) that "The program should either have been around for a while or be involved in research, or otherwise demonstrate an appeal beyond just its creator." --Numsgil 15:55, 15 November 2005 (UTC)

Until a product is completely done and released, I don't think it should go in this article. Again, Zelos, please try Numsgil's suggestion in creating an article called CELL before putting it into this article. Olorin28 02:41, 19 November 2005 (UTC)

Numsgil's criteria for inclusion are entirely reasonable. CELL doesn't appear to meet those criteria right now. Creating a CELL article first makes sense. --mb 03:30, 22 November 2005 (UTC)

Third Opinion: I really do side with Numsgil. I'm an inclusionist, but we must have SOME kind of standard for what demonstrates enough merit to be put in Wikipedia. Otherwise, you get vanity articles, things that purport to be important or meaningful or great that are either very new, limited, or absolute drivel. Zelos: If you want CELLS featured, demonstrate that it meets the criteria. Thesocialistesq 05:04, 25 December 2005 (UTC)

Spore
We probably should add Spore in the near-future.

Once it's out I see no reason why not. --Numsgil 07:58, 2 January 2006 (UTC)

Cleanup
WP is not a list of links. I had reorganized this list to match the format of other software lists--few categories, a simple bulletted list, no external links for bluelinked software, and removing of AfDed software. I was reverted. Please explain why this list should be different. --Karnesky 02:28, 20 February 2006 (UTC)


 * I did not mean to offend. I feel it works better in its present form, as it allows links to multiple aspects of a project.  Some simulators have wiki pages and websites, some have only websites, some have forums, etc.  Plus, this allows small blurbs to be written about each simulator if anyone decides to ever go that route.


 * My initial reaction was perhaps too hasty; I suspected well-intentioned but inept editing, especially with the removal of a link I did not think needed removing.


 * I am unfamiliar with what "AfDed" means.


 * --Numsgil 09:01, 20 February 2006 (UTC)


 * No offense taken, but I still think this page needs a cleanup. Why have off-site links if a simulator has a wiki page (and why put blurbs for those that have wiki pages too)?
 * Which link did you have a problem with me removing?
 * AfD="article for deletion." I deleted Breve (software), buy was apparently a little hasty--it hadn't been voted on, but had been speedy deleted.  See the deletion record.  It should've probably stayed in the list.  Sorry for the oversight.
 * I think the notable products on this page should be red-linked so that people will be encouraged to write articles about them. I also think a lot of external URLs should go (especially for software already in WP).  Let me know what you think. --Karnesky 10:47, 20 February 2006 (UTC)


 * How about a wiki link and one outside link/homepage? --Numsgil 19:44, 20 February 2006 (UTC)


 * The wiki links will typically include the outside link. If home pages move, they often get updated in the relevant wiki article, but NOT updated on the lists of software.  Also, a high number of links acts as a magnet for more spam links.  It would be an improvement to limit to one URL per product, but I think the cleanup-spam tag should stay on the article if you chose to do that.  WP is not a list of internal and especially not external links).  See the other software lists.  Most of them have removed as many external URLs as possible to help foster red links to have stubs written, but to minimize spam.  I see relatively few advantages to keeping so many links: why bother? --Karnesky 03:58, 21 February 2006 (UTC)


 * The problem is that the number of ALife simulators without wiki pages far outnumbers the number with wiki articles. If this were to change, then I'd see no reason not to reduce this list to a more common software list, but I personally don't want to write the missing articles.  Removing simulators without wiki pages hardly seems a proper solution.


 * This page was an outgrowth of the fact that there are atleast 3 or 4 different pages that had links to different ALife software that were all being maintained seperately and so were largely incongruent. I gathered and coordinated the data in the hopes that it would encourage more simulators to list themselves.  I'd support any initiatives that encourage that goal.  --Numsgil 15:38, 22 February 2006 (UTC)


 * But red links are O.K. and I think they are desirable here, as they indicate what articles are in demand. I never proposed removing simulators without wiki pages.  Do you have any objections to the cleanup I did, except for my deletion of Karnesky 21:06, 22 February 2006 (UTC)


 * Basically my concern is two fold: 1. If a simulator does not have a red link a page on it might not be forthcoming.  2.  If a simulator has only a red link the page becomes less useful than in its present form.  --Numsgil 17:47, 23 February 2006 (UTC)


 * Having red links stick around for an extended period of time isn't a problem. So, how about the changes I just made?  Breve (software) is back up & all red linked articles include a single external URL (and, actually, they only had one URL in your original list as well).  The only thing that is missing from your revision are the external URLs for blue links.  But those are all on the relevant article pages. --Karnesky 18:16, 23 February 2006 (UTC)


 * That is acceptable. --Numsgil 23:41, 23 February 2006 (UTC)

Cell Based
Added a new section for Cell based Alife simulations. Added Cell-O-Sim and Kyresoo Plants to this section. Note that the link now points directly to the plant simulation code. This code is fully functional and has been stable for over a year. Don't confuse it with the Kyresoo Gardening game, which is new and a long way from completion. Hellinar 29 May 2006


 * I think "cell based" begs the question of the ultimate organism representation (that is, the genotype and how it mutates). If I understand your website, it would seem to me that your sim is most closely related to parameter based simulations, like Darwinpond.  That is, each "cell" has a small list of numbers the control various phenotypes.


 * Would this be a correct assessment? --Numsgil 00:30, 30 May 2006 (UTC)


 * In a parameter based simulation like Darwinpond, the list of numbers directly controls the shape and behavior of phenotype. In Kyresoo, the list of numbers has no direct connection with the shape and behavior of the phenotype. Like the genetic information in a cell, it codes for the proteins expressed. These proteins determine the shape and behavior of the cell.


 * Most significantly, the proteins emitted also regulate the rate of their own production, and of other proteins in the system. These feedback loops break any direct link between the genetic code and the resulting behavior of the cell. In this, they are very different from parameter based systems. Not sure that “Cell based” is the best alternate heading for what Kyresoo and Cell-O-Sim capture though. Any alternatives to suggest?  --Hellinar 3 Jun 2006


 * Hmm, interesting. If I understand you right, you're saying that there's a larger disconnect between genotype and phenotype.  While "cell based" sims use parameter genotypes, the genotypes don't directly code the resulting phenotype, there's a few more steps invovled, which changes the order of complexity.


 * In light of this, perhaps we need to divise a way to also list this level of disconnect with the simulation in question? For instance, as a sub heading under paremeter based, have "phenotype based" and "genotype based" parameters, with phenotype based being Darwinpond etc. and "cell based" being the genotype based?  They still share the commonality of "numbers" being mutated, but differ in the level of complexity seperating these numbers and phenotype effects.  --Numsgil 06:25, 4 June 2006 (UTC)


 * Sounds reasonable. The main thing I am trying to distinguish is the direct parameter approach gene -> phenotype, and the multistage approach gene -> protein expression -> cell behavior -> phenotype.  But you could classify them both under parameter driven if you like. -- Hellinar 4 Jun 2006

e-den, a complete artificial evolution project
There are more programs: -:	helix4b, helix1, CoreLife. --- Derived from or leaned upon Tierra -:	Boppers --- [I never really understood, what's going on there, but it does have to do with artificial life] -:	Greenbanks Creature Behavior Simulator v1.45, by J. Greenbank. --- A predator / prey / food scheme simulation of the parameter class. aswell as lots of simulations with mere emphasis on flocking or boid-forming:
 * MFBoids3S, : CoolSchool (predator/prey-scheme),  : FlockDemo, :  A-Quarium1.0 and 2.0

....................................... Then, e-den (executable: eden60x) by Craig McColl, a program, which is - alas! - only a beta version, although fully playable, even if it has several minor bugs. It really must be mentioned here. It combines all of the possible features for a complete - and open ended in complexity - artificial evolution program: The Organisms have .. o:	a skeleton with up to 16 limbs of 8 different functions (hear, see, weapon, armor, eat, bend(!), signalling) o:	a neural net with hundred neurons, each with several dendrites and axons to variable orther neurons, thresholds o:	an energy reservoir gained by eating or winning in fight, needed to sustain metabolism or in fight o:	a metabolism reservoir, needed for reproduction o:	a movement-points household, gained along timeticks, needed to move o:	a friendlyness value, enabling the organism to decide, whether it should fight or breed with a confronted organism o:	all of the above generated by the organisms genetic information, their genome The 2d universe, the world, has grass and other organic material (made up of the 8 dead skeleton functions, so dead organisms contribute to the shape of the world or its climate) serving for different types of food aswell as one type of inorganic material (9-s), that constitute the inchangable (by running the world) shape that can deliberately be manually modified. The program has several features: o::  	The program handles genepools. Sexual and asexual reproduction, breeding and cloning are sustained. o::  	Mutation rate, climate, population-target, auto-repopulation can be set up. o::  	netsharing organisms by buffered email is possible (!). A major project of evolving networks of linked e-den worlds all over the world is possible. o::  	own organisms can be designed in the bug_lab (or even edited manually) and tested on their fitness for survival and viability e.g. on the included viable organisms (carnivores, herbivores, corals, explorer and some more). The minor bugs are: o::  	at reload of *.wld, part of the organisms instantly die for getting a negative "metab" when saving the world previously. This can be overcome by editing every saved world and replacing every "-" by nothing. An easy batch can do that for all saved worlds. o::  	(not a bug, but mentionned nowhere in the documentation:) inserting or loading organisms maybe even seems to go along with the chosen mutation rate, so if one wants to be sure to have a spore of the exactly same organism, one should put the mutation rate to 0, then resetting it to the desired value after having played one timetick with the inserted organisms. o::  	once connected to the internet, "frame with 9's" in order to prevent incoming organisms, is disabled in some constellations, and restarting the program and reloading the (unframed) world is necessary, if the world should be saved, framed with 9-s. [I still don't understand, what's really going wrong here .. at least "frame with 9's" is a bit queer to handle in the wanted way]

e-den was last updated in '99, when long term evolutions or very complex organisms run with it were still a long-winded task for machines under 1 GHz. The program fell to forgotteness, before its time had ever come and the author quit wanting to enhance further versions. Nowadays generation of several hundreds can be achieved in only few hours of permanent run and visible results in evolution detected. The deep aim of evolving artificial evolution around the planet by internet is more likely to possibly be achieved than earlier then. The only lacks, i found, are - in handling the program - that drawing and designing world shapes is very awkward, - in real-likeliness - only, that mutation rate is fix (only to be changed manually) whereas in nature mutation rate itself is subdued to (meta-) mutation, but that is very a subtle restriction to criticize (Have a look at the incredible real-likeliness of the carnivore samples, instead!). Then, many idle organisms just don't die for hundreds of thousands of timeticks, allowing idle worlds to run on and on seemingly for ever, making it necessary to either interfere or deliberately declaring such worlds infertile, while in nature billions of years may actually be necessary for changes in a stable equilibrium of life (but not of single organisms). But that's maybe not the fault of the program conception, but of nature ;-) Graphics are a little old fashion. The emphasis is rather on evolving species, than on learning. If a single organism has the ability to learn, depends on the evolution its species has taken up to now. e-den meets highest claims, I say. http://www.geocities.com/ResearchTriangle/Forum/3830/index.html http://www.geocities.com/ResearchTriangle/Forum/3830/edendownload.html e-den is freeware If you have questions or problems handling e-den or want to link your worlds online and exchange orgs by email, mail me: christof.held@t-online.de (the author - as I said - has quit working on the project years ago) christof held, 16:53, 26 August 2006 (UTC)

October 2006 Reorginization
I've moved some simulators around, if anyone has issues with any of the changes I've made, please tell me. I've also added Spore to the list, even though it isn't finished, because its inclusion helps explain what I mean by "module based" better than any other simulator I can think of. --Numsgil 20:21, 15 October 2006 (UTC)

Removed Impossible Creatures
I removed Impossible Creatures from this page. It was listed under module based simulators presumably because of the modularity of unit design. It is a real-time strategy game and not a simulator. I have never played the game, but it seems to me that unit design is basically designing a tool to defeat an opponent. I believe that if Impossible Creatures deserve a place here then so do a significant number of other videogames and that the inclusion of such would detract from the usefulness of this list. I intend no offense to whoever listed it. Af1218 20:22, 1 May 2007 (UTC)


 * This is sort of a grey area. ALife is more closely tied to entertainment purposes than many other sciences.  If someone could generate a list of games that might be included, maybe we could wade through them and make sense of which ones might be included.  Something like Spore goes in this category too.  It's not an alife simulator per se, but it definately has a great deal of alife-like qualities.  --Numsgil 20:36, 1 May 2007 (UTC)

Nov 20 Revert
After a great deal of discussion, it was decided that each simulator needs a wiki page to link to to be included. Framsticks is definately notable, and it should definately be included, but we need a wiki page at Framsticks to do so. --Numsgil (talk) 22:24, 20 November 2007 (UTC)
 * I'd like to see a Framsticks article. There are a few scholarly papers that reference it, which should be enough to kickstart a stub. Ideally we should track down some other printed reviews or articles too. Marasmusine (talk) 08:02, 21 November 2007 (UTC)

Simulators needing pages
These simulators should be added to the list once a wiki article is generated for them. Please add to the list if you're aware of any unlisted simulators.
 * Amoeba (Pargellis, A.N. 1996, Physica D 91:86-96)
 * Framsticks
 * Critterding —Preceding unsigned comment added by Bobken (talk • contribs) 17:24, 11 September 2008 (UTC)

transclusion
I note this entire article is transcluded at Artificial_life. This isn't proper. Either there is grounds for two separate articles, or there isn't, but not both at the same time. --dab (𒁳) 12:17, 4 December 2008 (UTC)
 * The Artificial Life article isn't exactly bulging at the seams, so I would support merging and redirecting this list. It would also be nice to find some reliable, independent sources for verification of the software that was re-added. Whilst we don't need full blown assertion of notability (a Nanopond article was deleted through AfD on those grounds, for example), we could do with some indication of importance so it doesn't turn into a directory of external links. Marasmusine (talk) 13:58, 4 December 2008 (UTC)


 * Merging it in to the ALife article is fine with me, too. I'd also second Marasmusine's concern about including external links: there's a very real chance of it getting polluted with lame projects.  --Numsgil (talk) 00:18, 6 December 2008 (UTC)

I've added a footnote to the "Living Code" link providing evidence of press coverage. Not sure about the notability of "micropond". "nanopond" appears to be notable only as the predecessor of micropond. --dab (𒁳) 16:19, 9 December 2008 (UTC)

ok, I realize that micropond/nanopond are probably not notable enough for mention in article body. I think they are still useful WP:EL material, and videos such as this are very illustrative of the topic. --dab (𒁳) 16:24, 9 December 2008 (UTC)
 * Rather than a list of external links to various Alife projects, perhaps just a single link to an existing directory, such as at the Open Directory Project . This would satisfy the WP:EL requirement that ELs be kept to a minimum, and those wishing to browse less-than-notable programs have links to well maintained lists. Marasmusine (talk) 18:11, 9 December 2008 (UTC)

Wikiproject Computing
I have removed the WikiProject tag, as this article is either a redirect or deleted. If you oppose, please restore the tag. Thank you, fahadsadah (talk,contribs) 15:57, 30 March 2009 (UTC)