OpenWorm

OpenWorm
software da free software (en)
Bayanai
Ƙaramin ɓangare na	digital organism (en)
Amfani	computer simulation (en)
Depicts (en)	Caenorhabditis elegans (mul)
Programmed in (en)	Python programming language
Source code repository URL (en)	https://github.com/openworm/OpenWorm
Software version identifier (en)	0.9.8, 0.7, 0.8, 0.9, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6 da 0.9.7
Shafin yanar gizo	openworm.org
Lasisin haƙƙin mallaka	MIT License (en)
Copyright status (en)	copyrighted (en)

OpenWorm wani aiki ne na kimiyya na duniya wanda aka yi don kwaikwayon tsutsar Caenorhabditis elegans a matakin ƙwayoyin halitta . ^{[1] [2]} Duk da cewa burin dogon lokaci shine a yi kwaikwayon dukkan ƙwayoyin C. elegans guda 959, mataki na farko shine a yi kwaikwayon motsin tsutsa ta hanyar kwaikwayon ƙwayoyin jijiyoyi 302 da ƙwayoyin tsoka 95. Al'ummar OpenWorm ce ke bin diddigin wannan kwaikwayon ƙasa-ƙasa.

Ya zuwa shekarar 2014, an gina injin kimiyyar lissafi mai suna Sibernetic don aikin kuma an ƙirƙiri samfuran haɗin jijiyoyi da ƙwayar tsoka a cikin tsarin NeuroML . Ana iya samun damar samfurin 3D na tsarin tsutsa ta hanyar yanar gizo ta hanyar burauzar OpenWorm. Aikin OpenWorm yana kuma bayar da gudummawa wajen haɓaka Geppetto, wani dandamali mai amfani da tsarin lissafi mai yawa wanda aka ƙera don tallafawa kwaikwayon dukkan halittu . ^[3]

Tsutsar da ke zagaye Caenorhabditis elegans wata cuta ce mai rai da rai, mai bayyananniyar cuta, kusan 1. tsawon mm, wanda ke rayuwa a cikin yanayin ƙasa mai zafi. Ita ce nau'in nau'in halittarsa kuma tana aiki a matsayin abin koyi ga fannoni daban-daban. ^[4]

C. elegans yana da ɗaya daga cikin tsarin jijiyoyi mafi sauƙi na kowace halitta - nau'in hermaphrodite ɗinsa yana da ƙwayoyin jijiyoyi 302 kacal. Bugu da ƙari, an tsara cikakken tsarin haɗin waɗannan ƙwayoyin jijiyoyi. Akwai ƙarancin ƙwayoyin halitta dubu ɗaya a cikin jikin tsutsar C. elegans, kuma saboda C. elegans wani tsari ne na halitta, kowannensu yana da takamaiman mai ganowa da kuma cikakkun rubuce-rubuce masu tallafawa. Kasancewar kwayar halitta ce mai tsari, an san kwayar halittar sosai, tare da wasu nau'ikan maye gurbi masu kyau da ake samu, da kuma cikakken wallafe-wallafen nazarin ɗabi'a. Da ƙarancin ƙwayoyin jijiyoyi da sabbin dabarun amfani da sinadarin calcium mai siffar photon guda biyu, nan ba da jimawa ba zai yiwu a yi rikodin cikakken aikin jijiyoyi na wani abu mai rai. Sarrafa ƙwayoyin jijiyoyi ta hanyar hanyoyin optogenetic, tare da ƙarfin fasaha da aka ambata a baya, ya samar da aikin wani matsayi mara misaltuwa - yanzu yana iya bayyana cikakken yanayin jijiyoyin jiki na dukkan halittu. ^[5]

Kokarin gina samfurin C. elegans a cikin silico, kodayake halitta ce mai sauƙi, ya haɓaka ci gaban fasahohin da za su sauƙaƙa kwaikwayon ƙwayoyin halitta masu rikitarwa a hankali.

Duk da cewa babban burin shine a kwaikwayi dukkan fasalulluka na halayen C. elegans, al'ummar OpenWorm da farko sun yi niyyar kwaikwayon amsawar motsi mai sauƙi: koya wa tsutsa rarrafe. Don yin haka, ana sanya tsutsar kama-da-wane a cikin yanayi na kama-da-wane. Daga baya an kafa cikakken madauri na amsawa: Ƙarfafa Muhalli > Canjin Jijiyoyi > Harbin Interneuron > Harbin Jijiyoyin Mota > Fitar da Mota > Canjin Muhalli > Canjin Jijiyoyi.

Akwai manyan ƙalubale guda biyu na fasaha a nan: yin kwaikwayon halayen jijiyoyi/na lantarki na kwakwalwa yayin da take sarrafa bayanai, da kuma yin kwaikwayon halayen injiniya na jiki yayin da take motsawa. Ana yin kwaikwayon halayen jijiyoyi ta hanyar samfurin Hodgkin-Huxley, kuma ana yin kwaikwayon halayen injin ta hanyar tsarin Smoothed Particle Hydrodynamics .

Ƙungiyar OpenWorm ta ƙera injin da ake kira Geppetto wanda zai iya haɗa waɗannan algorithms kuma saboda yanayinsa, za su iya yin kwaikwayon wasu tsarin halittu (kamar narkewar abinci ) waɗanda ƙungiyar za ta magance a wani lokaci daga baya.

Ƙungiyar ta kuma gina wani yanayi mai suna NeuroConstruct wanda ke iya fitar da tsarin jijiyoyi a cikin NeuroML . Ta amfani da NeuroConstruct, ƙungiyar ta sake gina cikakken haɗin C. elegans .^{[ana buƙatar hujja]}

Ta amfani da NeuroML, ƙungiyar ta kuma gina samfurin ƙwayar tsoka. Lura cewa waɗannan samfuran a halin yanzu suna yin kwaikwayon halayen da suka dace ne kawai don amsawar motsi mai sauƙi: halayen jijiyoyi/na lantarki da na inji da aka tattauna a sama.^{[ana buƙatar hujja]}

Mataki na gaba shine a haɗa wannan ƙwayar tsoka da ƙwayoyin jijiyoyi guda shida waɗanda ke haɗuwa a kai sannan a kimanta tasirinsu.

Tsarin da aka tsara shi ne a yi shi a matakai biyu:

• Kimanin synapses waɗanda ke haɗuwa akan waɗannan ƙwayoyin jijiyoyi
• Maimaita wannan tsari ga sauran ƙwayoyin tsoka

A shekarar 1998, masu bincike na Japan suka sanar da aikin Perfect C. elegans. An gabatar da wani tsari, amma da alama an yi watsi da aikin. ^{[6] [7]}

A shekara ta 2004, wata ƙungiya daga Hiroshima ta fara aikin Virtual C. elegans. Sun fitar da takardu guda biyu waɗanda suka nuna yadda kwaikwayonsu zai janye daga tallan kama-da-wane. ^{[8] [9]}

A shekara ta 2005, wani mai bincike a Texas ya bayyana wani na'urar kwaikwayo mai sauƙi ta C. elegans bisa ga hanyar sadarwa mai waya 1 wadda ta haɗa da na'urar sarrafa Parallax Basic Stamp ta dijital, abubuwan da ke shiga cikin ji da kuma abubuwan da ke fitowa daga injin. An yi amfani da na'urorin juyawa na A/D mai girman bit 16 da aka haɗa zuwa ƙwayoyin jijiyoyi masu aiki da aka kwaikwayi amplifier da kuma na'urar firikwensin zafin waya 1. An sarrafa fitowar injin ta hanyar amfani da na'urori masu auna karfin dijital mai matsayi 256 da kuma tashoshin dijital mai girman bit 8. Aikin tsoka na wucin gadi ya dogara ne akan masu kunna Nitinol. Ya yi amfani da madauri na aiki na "ji-tsari-amsa" wanda ya sake ƙirƙirar halaye da dama na ɗabi'a.

An soki waɗannan yunƙurin farko na kwaikwayon da rashin kasancewa gaskiya a fannin halitta. Duk da cewa muna da cikakken haɗin ginin, ba mu san nauyin synaptic a kowace synapse da aka sani ba. Ba ma san ko synapses ɗin suna hana ko kuma suna tayar da hankali ba . Domin rama wannan, ƙungiyar Hiroshima ta yi amfani da na'urar koyon na'ura don nemo wasu nauyin synapses waɗanda zasu haifar da ɗabi'ar da ake so. Saboda haka ba abin mamaki ba ne cewa samfurin ya nuna ɗabi'ar, kuma ƙila ba zai iya wakiltar ainihin fahimtar tsarin ba.^{[ana buƙatar hujja]}

Al'ummar OpenWorm ta himmatu ga manufofin kimiyya a buɗe . Gabaɗaya wannan yana nufin cewa ƙungiyar za ta yi ƙoƙarin bugawa a cikin mujallun da ke buɗe kuma ta haɗa da duk bayanan da aka tattara (don guje wa matsalar aljihun fayil ). Hakika, duk bayanan halitta da ƙungiyar ta tattara suna nan a bainar jama'a.

Kafin tsakiyar shekarar 2024, ana samun littattafai ashirin da ƙungiyar ta wallafa kyauta a shafinta na yanar gizo. Duk manhajojin da OpenWorm ta samar kyauta ne kuma a bude suke.

1. ↑ Palyanov, Andrey; Khayrulin, Sergey; Larson, Stephen D.; Dibert, Alexander (2012-01-01). "Towards a virtual C. elegans: A framework for simulation and visualization of the neuromuscular system in a 3D physical environment". In Silico Biology (in Turanci). 11 (3): 137–147. doi:10.3233/isb-2012-0445. ISSN 1386-6338. PMID 22935967.
2. ↑ Gewaltig, Marc-Oliver; Cannon, Robert (2014-01-23). "Current Practice in Software Development for Computational Neuroscience and How to Improve It". PLOS Computational Biology (in Turanci). 10 (1). Bibcode:2014PLSCB..10E3376G. doi:10.1371/journal.pcbi.1003376. ISSN 1553-7358. PMC 3900372. PMID 24465191.
3. ↑ Takahashi, Dean (30 April 2014). "Openworm is going to be a digital organism in your browser". VentureBeat. Archived from the original on 4 July 2017. Retrieved 7 September 2017.
4. ↑ Sudhaus W, Kiontke K (2009). "Phylogeny of Rhabditis subgenus Caenorhabditis (Rhabditidae, Nematoda)". Journal of Zoological Systematics and Evolutionary Research. 34 (4): 217–233. doi:10.1111/j.1439-0469.1996.tb00827.x.
5. ↑ "Getting Started". openworm.org. Retrieved 2026-05-17.
6. ↑ Kitano, Hiroaki; Hamahashi, Shugo; Luke, Sean (April 1998). "The Perfect C. ELEGANS Project: An Initial Report". Artificial Life (in Turanci). 4 (2): 141–156. CiteSeerX 10.1.1.25.8565. doi:10.1162/106454698568495. ISSN 1064-5462. PMID 9847421. S2CID 12383326.
7. ↑ Kaufman, Jeff (2 November 2011). "Whole brain emulation and nematodes".
8. ↑ Suzuki, Michiyo; Goto, Takeshi; Tsuji, Toshio; Ohtake, Hisao (2005). "A dynamic body model of the Nematode C. elegans with neural oscillators" (PDF). Journal of Robotics and Mechatronics. 17 (3): 318–326. doi:10.20965/jrm.2005.p0318.
9. ↑ Suzuki, Michiyo; Tsuji, Toshio; Ohtake, Hisao (September 2005). "A model of motor control of the nematode C. elegans with neuronal circuits" (PDF). Artificial Intelligence in Medicine. 35 (1–2): 75–86. doi:10.1016/j.artmed.2005.01.008. ISSN 0933-3657. PMID 16084704.