From Simple Regulatory Motifs to Parallel Model Checking of Complex Transcriptional Networks
| BARNAT, Jiří, Luboš BRIM, Ivana ČERNÁ, Sven DRAŽAN and David ŠAFRÁNEK. From Simple Regulatory Motifs to Parallel Model Checking of Complex Transcriptional Networks. In Proceedings of PDMC 2008 - Parallel and Distributed Methods ins VerifiCation. Budapest: Ivana Cerna and Gerald Luettgen, 2008, p. 83-96, 15 pp. ISSN 1571-0661. |
|
Other formats:
BibTeX
LaTeX
RIS
|
| Basic information | |
|---|---|
| Original name | From Simple Regulatory Motifs to Parallel Model Checking of Complex Transcriptional Networks |
| Name in Czech | Od jednoduchých regulačních motivů k ověřování komplexních transkripčních sítí |
| Authors | BARNAT, Jiří (203 Czech Republic), Luboš BRIM (203 Czech Republic), Ivana ČERNÁ (203 Czech Republic), Sven DRAŽAN (203 Czech Republic) and David ŠAFRÁNEK (203 Czech Republic, guarantor). |
| Edition | Budapest, Proceedings of PDMC 2008 - Parallel and Distributed Methods ins VerifiCation, p. 83-96, 15 pp. 2008. |
| Publisher | Ivana Cerna and Gerald Luettgen |
| Other information | |
|---|---|
| Original language | English |
| Type of outcome | Proceedings paper |
| Field of Study | 10201 Computer sciences, information science, bioinformatics |
| Country of publisher | Czech Republic |
| Confidentiality degree | is not subject to a state or trade secret |
| RIV identification code | RIV/00216224:14330/08:00024175 |
| Organization unit | Faculty of Informatics |
| ISSN | 1571-0661 |
| Keywords in English | transcriptional networks; model checking; B. subtilis |
| Tags | B. subtilis, Model checking, transcriptional networks |
| Tags | International impact, Reviewed |
| Changed by | Changed by: prof. RNDr. Ivana Černá, CSc., učo 1419. Changed: 31/3/2010 15:34. |
| Abstract |
|---|
| The central mechanism which drives every living cell is protein synthesis, the so-called transcription, which is realized according to the genetic code. There are complex regulatory interactions that control transcription of genes to proteins. Owing to their inherent complexity, analysis of dynamical models of such interactions requires a scalable computational approach. In this paper we employ parallel LTL model checking for a case study of selected dynamic properties of an in silico model of transcription in Bacillus subtilis, a bacterium living in soil. Moreover, we show the general fact that crucial LTL properties characterising transcriptional dynamics can be inferred from network motifs commonly studied in systems biology. |
| Abstract (in Czech) |
|---|
| Centrálním mechanismem, jenž řídí funkčnost každého živého organismů, je syntéza proteinů, tzv. transkripce, realizovaná dle genetického kódu. Transkripce je řízena netriviálními interakcemi na biochemické bázi, které ovlivňují míru transkripce jednotlivých proteinů. Analýza dynamických aspektů transkripce na úrovni in silico modelů tudíž vyžaduje škálovatelné výpočetní metody. V tomto článku je ukázáno, jak inherentní vlastnosti transkripčních mechanismů (identifikovány prostřednictvím určitých motivů) lze analyzovat na úrovni abstraktního kvalitativního modelu prostřednictvím metody ověřování modelů. Použití metody je demonstrováno na analýze transkripce proteinů zajišťujících sporulaci bakterie Bacilus subtilis. |
| Links | |
|---|---|
| MSM0021622419, plan (intention) | Name: Vysoce paralelní a distribuované výpočetní systémy |
| Investor: Ministry of Education, Youth and Sports of the CR, Highly Parallel and Distributed Computing Systems | |
| 1ET408050503, research and development project | Name: Techniky automatické verifikace a validace softwarových a hardwarových systémů |
| Investor: Academy of Sciences of the Czech Republic, Techniques for automatic verification and validation of software nad hardware systems | |
| 1M0545, research and development project | Name: Institut Teoretické Informatiky |
| Investor: Ministry of Education, Youth and Sports of the CR, Institute for Theoretical Computer Science | |
PrintDisplayed: 25/4/2024 11:40