Workshop on Operations Research of Biological Systems

Administration

Description

Aim of the workshop

The workshop on the emerging field of biological operations research – the application of operations research methodologies in systems and molecular cell biology – is designed to bring together participants and lecturers versed in either of the two disciplines that are eager to further uncover the deep connections between the two fields and find new avenues for research and collaboration while gaining new insight on biological functions from an operational and system perspective.

The long-term goal of the workshop is to boost research and collaboration in this field, by acquainting researchers with the existing long-standing problems in system biology, molecular cell biology and bacterial physiology.

We will explore the deep connections between these problems and those that arise in operations research, e.g. the question of regulation of mass production in an uncertain market, dynamic resource allocation, scheduling problems and the impact of different queuing disciplines of speed and efficiency of a complex production facility.

Researchers will have a chance to exchange ideas and compare different methodologies and modes of thinking about operational parameters such as throughput, efficiency, resource allocation, reliability, redundancy, and cost in a novel biological context.

Topics

Scheduling and queuing disciplines – from circadian rhythms to pipelining of self-replication
Allocation of resources to self-replication vs. maintenance

Transcription and translation regulation, role of external and internal information
Controlling WIP (work-in-progress) – Kanban, TOC, and CONWIP vs. product feedback inhibition
Anticipatory systems and their reverse engineering
Metabolic networks and queuing theory
Bullwhip effect and the role of inventory control, forecasting and information
Modern queuing theory
Self-regulating and resource dependent branching processes

Material

General Information List of Participants Poster group photo

Workshop on Operations Research of Biological Systems | (smr 3223)

Go to day

Monday, 9 July 2018

08:30 - 20:00 Monday, 9 July

08:30 Registration and Administrative formalities 1h0'

Slot reserved for Participants not staying in ICTP Guesthouses & Speakers only.
(Participants staying in ICTP Guesthouses are registered upon check-in at the Guesthouse Reception desks.)
AFTER having registered, Visitors funded by the ICTP must collect their dues at the Operations & Travel Unit Office c/o E. Fermi building, ground floor (open Mon., Tue. &  Fri. only, 8:30-12:00/13:30-14:30).

09:30 Opening and Welcome address 15' ( Leonardo Building - Euler Lecture Hall )
09:45 Introduction - Bacterial Cell as a Factory - A Self-Replicating Queuing Network Model for Cellular Growth 1h0'

Speaker: Rami PUGATCH (Ben Gurion U. / ICTP)
10:45 Sculpted by Self-Replication 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: Shlomi REUVENI (Tel Aviv University)

11:45 What’s Love Got To Do with It? Stable Marriage Problem Approach to Modeling Diauxic Growth in Microbial Ecosystems 1h0'

Speaker:	Sergei MASLOV (U. of Illinois at Urbana-Champaign)
Material:	Slides

12:45 Lunch break 1h15' ( Leonardo Building - Cafeteria )
14:00 Inference of Response and Latent State of a Multitype Age-Structured Population from Cell Lineage Trees 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: Tetsuya KOBAYASHI (Tokyo University)
15:00 Mathematical Models of Bacterial Growth and Division 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: Sanjay JAIN (University of Delhi)
16:00 Coffee break 30' ( Leonardo Building - Terrace )
16:30 Lineages, Growth, and Selection in Heterogeneous Populations 1h0'

Speaker: Edo KUSSELL (NYU)
19:00 Welcome reception 1h0' ( Leonardo Building - Terrace )

Tuesday, 10 July 2018

09:00 - 17:30 Tuesday, 10 July

09:00 The Partition Principle for Risk Management: A Common Theme Underlying many Approaches? 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: John BECHHOEFER (Simon Fraser University)
10:00 Coffee break 30' ( Leonardo Building - Terrace )

10:30 A Very Basic Queueing Theory Tutorial 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker:	Mor HARCHOL-BALTER (Carnegie Mellon University)
Material:	Slides

11:30 Protein Folding Matters to the Cell: For its Growth Laws, Aging, Evolution, and Maybe Origins 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: Ken DILL (Stony Brook University)
12:30 Lunch break 1h30' ( Leonardo Building - Cafeteria )
14:00 Extended discussion session 2h0' ( QLS Section, 2nd floor, old SISSA building )
16:00 Coffee break 30' ( Central Area, 2nd floor, old SISSA building )
16:30 Extended discussion session 1h0' ( QLS Section, 2nd floor, old SISSA building )

Wednesday, 11 July 2018

09:00 - 18:00 Wednesday, 11 July

09:00 A Unification of Resource Competition Models: Chemostat, Nutrient Limitations and Self-building Spatial Heterogeneity 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker:	Li ZHIYUAN (Princeton)
Material:	Slides

10:00 Coffee break 30' ( Leonardo Building - Terrace )
10:30 Geometric Queueing Theory 1h0'

Speaker: Eitan BACHMAT (Ben Gurion U.)
11:30 Cellular Exploratory Adaptation 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: Naama BRENNER (Technion)
12:30 Lunch break 1h30' ( Leonardo Building - Cafeteria )
14:00 Ribosome Self Assembly Leads to Overlapping Reproduction Cycles and Increases Growth Rate 1h0'

Speaker: Rami PUGATCH (Ben Gurion U. / ICTP)
15:00 The Origin of Schaechter, Maaløe, Kjeldgaard 1958 1h0'

Speaker: Suckjoon JUN (UCSD)
16:05 Coffee break 25' ( Leonardo Building - Terrace )
16:20 Group Photo 5' ( Main Entrance (Leonardo Building) )

16:30 ICTP COLLOQUIUM on "Neural Networks and Gene Regulatory Networks with Product Form Solutions" 1h30' ( Leonardo Building - Budinich Lecture Hall )

Speaker:	Erol GELENBE (Imperial College, London)
Material:	colloquium web page

Thursday, 12 July 2018

09:00 - 18:30 Thursday, 12 July

09:00 G-Networks: Solvable Probability Models of Gene Regulatory, as well as Spiking Neural Networks 1h0'

Speaker: Erol GELENBE (Imperial College, London)
10:00 Coffee break 30' ( Leonardo Building - Terrace )

10:30 Individuality in Bacterial Growth Homeostasis 1h0'

Speaker:	Hanna SALMAN (University of Pittsburgh)
Material:	Slides

11:30 Diffusion Approximations for Controlled Queuing Systems 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: Amarjit BUDHIRAJA (University of North Carolina)
12:30 Lunch break 1h30' ( Leonardo Building - Cafeteria )
14:00 Extended discussion session 2h0' ( QLS Section, 2nd floor, old SISSA building )
16:00 Coffee break 30' ( Terrace, Leonardo building )
16:30 Extended discussion session 1h0' ( QLS Section, 2nd floor, old SISSA building )

Friday, 13 July 2018

09:00 - 13:15 Friday, 13 July

09:00 Cooperative Search Games 1h0' ( Leonardo Building - Euler Lecture Hall )

Speaker: Antonio CELANI (ICTP)
10:00 Coffee break 30' ( Leonardo Building - Terrace )
10:30 Molecular Traffic Regulation on Nucleic Acid Strands: Signals, Programmed Errors and Recoding 45' ( Leonardo Building - Euler Lecture Hall )

Speaker: Bhavya MISHRA, Indian Institute of Technology Kanpur

11:15 Characterizing Steady States of Genome-Scale Metabolic Networks in Continuous Cell Cultures 45'

Speaker:	Roberto MULET GENICIO, University of Havana
Material:	Slides

12:00 Concluding remarks 30'