Inferring Biological Regulatory Networks from Process Hitting models - PowerPoint PPT Presentation

— MOVEP’2012 — 10 th School for young researchers about Modelling and Verifying Parallel processes Inferring Biological Regulatory Networks from Process Hitting models Maxime FOLSCHETTE 1 , 2 MeForBio / IRCCyN / École Centrale de Nantes (Nantes, France) maxime.folschette@irccyn.ec-nantes.fr http://www.irccyn.ec-nantes.fr/~folschet/ Joint work with: Loïc PAULEVÉ, Katsumi INOUE, Morgan MAGNIN, Olivier ROUX

Inferring BRNs from PH models ◦ Introduction Context and Aims MeForBio team: Algebraic modeling to study complex dynamical biological systems Maxime FOLSCHETTE 2/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Introduction Context and Aims MeForBio team: Algebraic modeling to study complex dynamical biological systems 1) Two main models • Historical model: Biological Regulatory Network (René Thomas) • New developed model: Process Hitting 2) Allow efficient translation from Process Hitting to BRN Maxime FOLSCHETTE 2/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Maxime FOLSCHETTE 3/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 Maxime FOLSCHETTE 3/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 0 , b 1 , z 0 � Maxime FOLSCHETTE 3/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 0 , b 1 , z 0 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 0 , b 1 , z 1 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 1 , b 1 , z 1 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 1 , b 1 , z 2 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort to express ab a 1 ∧ b 0 Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort to express ab a 1 ∧ b 0 Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Adding cooperations [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort to express ab a 1 ∧ b 0 Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Advantage: regular sort; drawbacks: complexity, temporal shift Maxime FOLSCHETTE 4/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Static analysis: successive reachability [PMR12-MSCS] Successive reachability of processes: b d 2 2 a 1 1 1 0 0 0 c 0 1 Maxime FOLSCHETTE 5/16 MOVEP’2012 — 2012/12/06

Inferring BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting Static analysis: successive reachability [PMR12-MSCS] Successive reachability of processes: b d 2 2 a • Initial context 1 1 1 � a 1 , { b 0 , b 1 } , c 0 , z 0 � 0 0 0 c 0 1 Maxime FOLSCHETTE 5/16 MOVEP’2012 — 2012/12/06