{"id":12130,"date":"2021-01-13T09:30:00","date_gmt":"2021-01-13T11:30:00","guid":{"rendered":"https:\/\/mindthegraph.com\/blog\/?p=12130"},"modified":"2022-10-18T08:09:26","modified_gmt":"2022-10-18T11:09:26","slug":"pyscratch-spatial-and-temporal-information-from-scratch-assays","status":"publish","type":"post","link":"https:\/\/mindthegraph.com\/blog\/lt\/pyscratch-spatial-and-temporal-information-from-scratch-assays\/","title":{"rendered":"PyScratch: Naujas \u012frankis erdvinei ir laiko informacijai i\u0161 \"Scratch\" tyrim\u0173 apdoroti"},"content":{"rendered":"

PyScratch - tai nauja atvirojo kodo programin\u0117 \u012franga, \u012fdiegta Python kalba, skirta migracijos duomen\u0173 analizei, turinti patogi\u0105 s\u0105saj\u0105, leid\u017eian\u010di\u0105 ja naudotis mokslininkams, neturintiems programavimo \u012fg\u016bd\u017ei\u0173 arba turintiems j\u0173 visai nedaug. <\/p>\n\n\n\n

Programin\u0117 \u012franga sukurta 2017 m. bendradarbiaujant trims Brazilijos mokslininkams, dirbantiems Kampinaso universiteto NanoCell Interactions laboratorijoje. <\/p>\n\n\n\n

Ji gim\u0117 i\u0161 \u0161i\u0173 mokslinink\u0173 poreikio, o \u0161iandien \u0161ios programin\u0117s \u012frangos tikslas - palengvinti kasdien\u0119 mokslinink\u0173 praktik\u0105, atsisakyti rankin\u0117s analiz\u0117s, padidinti atkuriamum\u0105 ir suma\u017einti \u017emogi\u0161k\u0105sias klaidas.<\/p>\n\n\n\n

\"\"<\/a><\/figure><\/div>\n\n\n\n

Vaizd\u0173 analiz\u0117 yra vienas svarbiausi\u0173 b\u016bd\u0173, kur\u012f mokslininkai naudoja \u012fvairiose metodikose rezultatams analizuoti. <\/p>\n\n\n\n

Pastaraisiais metais padid\u0117jo ne tik automatini\u0173 mikroskop\u0173 naudojimo apimtis, bet ir gaunam\u0173 duomen\u0173 sud\u0117tingumas. <\/p>\n\n\n\n

Dalis mokslininko darbo - atrasti, kaip elgtis su naujos r\u016b\u0161ies informacija, be to, analizuoti ir apdoroti duomenis. <\/p>\n\n\n\n

Tam mokslininkams reikia ger\u0173 ir specializuot\u0173 priemoni\u0173, kad jie gal\u0117t\u0173 teisingai i\u0161gauti ir interpretuoti visus duomenis.<\/p>\n\n\n\n

Pirm\u0105 kart\u0105 PyScratch buvo sukurta siekiant pad\u0117ti biologei tyr\u0117jai Fernandai Garsijai-Fosai analizuoti did\u017eiul\u012f migracijos tyrim\u0173 duomen\u0173 kiek\u012f. <\/p>\n\n\n\n

\"Atlikau v\u0117\u017eini\u0173 l\u0105steli\u0173 \u012fbr\u0117\u017eim\u0105 ir inkubavau \u012frangoje 48 valandas, kas 15 minu\u010di\u0173 darydamas nuotraukas, ir tik vieno eksperimento pabaigoje tur\u0117jau apie t\u016bkstant\u012f nuotrauk\u0173, kurias gal\u0117jau per\u017ei\u016br\u0117ti ir i\u0161analizuoti! <\/p>\n\n\n\n

Rankiniu b\u016bdu to padaryti buvo ne\u012fmanoma\", - sako M. Garcia-Fossa. Nor\u0117dama i\u0161spr\u0119sti \u0161i\u0105 problem\u0105, Garcia-Fossa kreip\u0117si pagalbos \u012f savo partner\u012f, fizik\u0105 Vladimir\u0105 Gaal\u0105, kuris tuo metu mok\u0117si \"Python\", ir tai buvo puiki proga pritaikyti \u0161ias \u017einias prakti\u0161kai.<\/p>\n\n\n\n

Taigi abu jie dirbo sprendime naudodami \"Python\" program\u0105, kuri atpa\u017eino subrai\u017eytas sritis ir eksportavo \u012f csv fail\u0105. <\/p>\n\n\n\n

\"Laikui b\u0117gant pajutome b\u016btinyb\u0119 sukurti vartotojo s\u0105saj\u0105, kad b\u016bt\u0173 dar lengviau naudotis, taip gal\u0117tume paskelbti programin\u0119 \u012frang\u0105 bet kuriam tyr\u0117jui, kuriam taip pat reikia naudoti\", - sako Garcia-Fossa apie programin\u0117s \u012frangos straipsn\u012f, kur\u012f galite patikrinti. Spauskite \u010dia<\/a>.<\/p>\n\n\n\n

Garcia-Fossa taip pat pasakoja, kad jiems prireik\u0117 nema\u017eai laiko, kol i\u0161 nuotrauk\u0173 atpa\u017eino ir nustat\u0117 migracijos teritorij\u0105, nes nuotraukos gali labai skirtis viena nuo kitos d\u0117l \u0161viesos, fokusavimo ir kontrasto, o \u0161iandien naudojama versija jau gali gana gerai analizuoti. <\/p>\n\n\n\n

Nepaisant to, jie vis dar tobulina programin\u0119 \u012frang\u0105, leisdami naujas ir geresnes versijas, nes paskelbtame straipsnyje d\u0117l naudotoj\u0173 poreikio buvo i\u0161kelta keletas patobulinim\u0173.<\/p>\n\n\n\n

Programin\u0117s \u012frangos veikimui patvirtinti naudojamas migracijos, \u012fbr\u0117\u017eim\u0173 arba \u017eaizd\u0173 gijimo bandymas yra biologijoje da\u017enai naudojamas bandymas, nes juo galima analizuoti pagrindin\u012f fiziologini\u0173 ir patologini\u0173 l\u0105steli\u0173 \u012fvyki\u0173 mechanizm\u0105. <\/p>\n\n\n\n

\u017daizd\u0173 gijimo tyrimai yra svarbus b\u016bdas suprasti ne tik angiogenez\u0119 ir navik\u0173 vystym\u0105si, bet ir vystym\u0105si bei audini\u0173 modeliavim\u0105. <\/p>\n\n\n\n

Kai tyrimas atliekamas dvimat\u0117je erdv\u0117je, galima i\u0161matuoti, kaip greitai l\u0105stel\u0117s reaguoja \u012f \u017eaizd\u0105, apiman\u010di\u0105 apibr\u0117\u017et\u0105 plot\u0105.<\/p>\n\n\n\n

Kitaip tariant, eksperimentas i\u0161 esm\u0117s yra toks: sukurkite ply\u0161\u012f konfluencini\u0173 l\u0105steli\u0173 monosluoksnyje, esan\u010diame plok\u0161tel\u0117je. <\/p>\n\n\n\n

Laikui b\u0117gant l\u0105stel\u0117s pradeda migruoti, kad u\u017epildyt\u0173 tarp\u0105, ir galima i\u0161matuoti l\u0105steli\u0173 migracijos greit\u012f. <\/p>\n\n\n\n

Tada, norint i\u0161matuoti l\u0105steli\u0173 migracijos greit\u012f, reikia gauti vaizd\u0173, j\u0173 daugyb\u0119, o tai savo ruo\u017etu yra problemi\u0161kas analiz\u0117s etapas, nes reikia matuoti rankiniu b\u016bdu. <\/p>\n\n\n\n

Laimei, \u0161iandien turime daugyb\u0119 technologij\u0173, kuriomis galime tobulinti ir modernizuoti savo analiz\u0117s proces\u0105, tod\u0117l mokslininkai gali taikyti geresnius ir labiau individualizuotus b\u016bdus rezultatams gauti. <\/p>\n\n\n\n

Kaip tai padar\u0117 Garcia-Fossa ir Gaalas.<\/p>\n\n\n\n

\u0160iandien galima rasti kit\u0173 komercini\u0173 ir nekomercini\u0173 priemoni\u0173, skirt\u0173 \u017eaizdos vietai apdoroti. <\/p>\n\n\n\n

Ta\u010diau jie n\u0117ra tokie paprasti, kaip PyScratch, ir reikalauja i\u0161 naudotojo tam tikro programavimo lygio, taip pat reikalauja nuolatinio naudotojo d\u0117mesio, tod\u0117l analiz\u0117 tampa labiau jautri \u017emogi\u0161koms klaidoms, be to, tyr\u0117jas sugai\u0161ta laiko, kad i\u0161analizuot\u0173 visas nuotraukas ir duomenis.<\/p>\n\n\n\n

Straipsnyje autoriai paai\u0161kina, kaip veikia programin\u0117 \u012franga. I\u0161 vis\u0173 eksperimento metu padaryt\u0173 nuotrauk\u0173 naudotojas gauna kableliais atskirt\u0173 reik\u0161mi\u0173 (comma-separated values, .cvs) fail\u0105 - i\u0161vest\u012f, kurioje lentel\u0117s duomenys saugomi paprastu tekstu. <\/p>\n\n\n\n

Tada naudotojas gali apdoroti duomenis \u012fprasta tvarka. Garcia-Fossa sako, kad programa buvo labai svarbi jos magistro darbui: \"Programin\u0117 \u012franga transformuoja \u012fvesties duomenis \u012f biologin\u0119 prasm\u0119 turin\u010di\u0105 vert\u0119, pavyzd\u017eiui, l\u0105steli\u0173 migracijos greit\u012f. <\/p>\n\n\n\n

\"PyScratch\" d\u0117ka gal\u0117jau geriau i\u0161analizuoti savo nanodaleli\u0173 poveik\u012f prostatos v\u0117\u017eio l\u0105stel\u0117ms, i\u0161matuoti l\u0105steli\u0173 migracijos greit\u012f ir tiksl\u0173 laik\u0105, per kur\u012f jos gerai u\u017esidaro.\"<\/p>\n\n\n\n

\"\"<\/a><\/figure><\/div>\n\n\n\n

Jei norite i\u0161bandyti \"PyScratch\" savo tyrimams, \u0161i programin\u0117 \u012franga yra laisvai prieinama ir visi mokslo bendruomen\u0117s nariai gali ja naudotis, pad\u0117dami Garsijai-Fosai ir Gaalui tobulinti ir gerinti program\u0105.<\/p>\n\n\n\n

 ____<\/p>\n\n\n\n

Kaip kol kas sekasi naudotis Mind the Graph? Pad\u0117kite mums tobulinti m\u016bs\u0173 platform\u0105 jums ir daugeliui kit\u0173 mokslinink\u0173 paskelbdami Mind the Graph ap\u017evalg\u0105. Papasakokite mums apie savo patirt\u012f, tiesiog spustel\u0117kite \u010dia<\/a>. <\/p>","protected":false},"excerpt":{"rendered":"

PyScratch - tai nauja atvirojo kodo programin\u0117 \u012franga, \u012fdiegta Python kalba, skirta migracijos duomen\u0173 analizei, turinti patogi\u0105 s\u0105saj\u0105, leid\u017eian\u010di\u0105 ja naudotis mokslininkams, neturintiems programavimo \u012fg\u016bd\u017ei\u0173 arba turintiems j\u0173 visai nedaug. Programin\u0117 \u012franga buvo sukurta 2017 m. bendradarbiaujant trims Brazilijos mokslininkams Kampinaso universiteto NanoCell Interactions laboratorijoje. Ji buvo [...]<\/p>","protected":false},"author":4,"featured_media":12133,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[959,28],"tags":[817,554,964],"yoast_head":"\nA new tool for processing spatial and temporal information<\/title>\n<meta name=\"description\" content=\"Read this blog to know what PyScratch is and how that new tool processes spatial and temporal information from scratch assays.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/mindthegraph.com\/blog\/lt\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/\" \/>\n<meta property=\"og:locale\" content=\"lt_LT\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A new tool for processing spatial and temporal information\" \/>\n<meta property=\"og:description\" content=\"Read this 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He has a Ph.D. and solid scientific background in Psychopharmacology and experience as a Guest Researcher at the Max Planck Institute of Psychiatry (Germany) and Researcher in D'Or Institute for Research and Education (IDOR, Brazil). Fabricio holds over 2500 citations in Google Scholar. He has 10 years of experience in small innovative businesses, with relevant experience in product design and innovation management. Connect with him on LinkedIn - Fabricio Pamplona.","sameAs":["http:\/\/mindthegraph.com","https:\/\/www.linkedin.com\/in\/fabriciopamplona"],"url":"https:\/\/mindthegraph.com\/blog\/lt\/author\/fabricio\/"}]}},"_links":{"self":[{"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/posts\/12130"}],"collection":[{"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/comments?post=12130"}],"version-history":[{"count":1,"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/posts\/12130\/revisions"}],"predecessor-version":[{"id":12134,"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/posts\/12130\/revisions\/12134"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/media\/12133"}],"wp:attachment":[{"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/media?parent=12130"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/categories?post=12130"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/lt\/wp-json\/wp\/v2\/tags?post=12130"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}