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Evolutionary Systems Biology Group - Homepage
This is the homepage of the Evolutionary Systems Biology Group at the University of Wisconsin-Madison. It gives an overview of group members, research, news, events and other group info.
Group Meetings Summer 2012
Please email Laurence Loewe, if you would like to present here.
| Date | Time+Place | Presenter | Topic | Mod |
Farm |
News |
Scr |
Jest | Tim |
|---|---|---|---|---|---|---|---|---|---|
| Mon, 28 Jan 2013 |
1:15-2:45pm, WID room 3160 | Seth Keel |
The galactose network |
IFL |
KE |
KE |
|||
| Mon, 4 Feb 2013 | 1:15-2:45pm, WID room 3160 | Bob Mau |
Quantifying diversity |
IFL | KE | KE | |||
| Mon, 11 Feb 2013 | 1:15-2:45pm, WID room 3160 | Discussion: LL+All | Evolvix Internal Representation |
IFL | KE | KE | |||
| Mon, 18 Feb 2013 | 1:15-2:45pm, WID room 3160 | Discussion: LL+All | Evolvix Internal Representation; please plan to go to talk by El-Samad. |
IFL | KE | KE | |||
| Mon, 18 Feb 2013 |
3:30-4:30pm, Ebling Symposium Center |
Hana El-Samad |
From Symthetic Biology to Systems Analyses and Back: Probing the Organizational Principles of Cellular Stress Responses |
||||||
| Mon, 25 Feb 2013 | 1:15-2:45pm, WID room 3160 | Discussion: LL+All | Evolvix Internal Representation | IFL | KE | KE | |||
| Mon, 4 Mar 2013 | 1:15-2:45pm, WID room 3160 | Steve Goldstein |
CA Statistics |
IFL | KE | KE | |||
| Mon, 11 Mar 2013 | 1:15-2:45pm, WID room 3160 | Kurt Ehlert |
Clustering Gene Expression Patterns |
IFL | KE | KE | |||
| Mon, 18 Mar 2013 | 1:15-2:45pm, WID room 3160 | Laurence Loewe |
Evolvix Internal Representation |
IFL | KE | KE | |||
| Mon, 25 Mar 2013 | Spring Break |
- |
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| Mon, 1 Apr 2013 | 1:15-2:45pm, WID room 3160 | Seth Keel |
Muller's ratchet |
IFL | KE | KE | |||
| Mon, 8 Apr 2013 | No meeting |
--- |
|
IFL | KE | KE | |||
| Mon, 15 Apr 2013 | 1:15-2:45pm, WID room 3160 | Laurence Loewe |
How to efficiently simulate Muller's ratchet and a note on Galaxy. |
IFL | KE | KE | |||
| Mon, 22 Apr 2013 | 1:15-2:45pm, WID room 3160 | Steve Goldstein |
CA Statistics latest progress |
IFL | KE | KE | |||
| Mon, 29 Apr 2013 | 1:15-2:45pm, WID room 3160 | Iratxo Flores-Lorca |
CVODE... |
IFL | KE | KE | |||
| Mon, 6 May 2013 | 1:15-2:45pm, WID room 3160 | ? |
Michael Whitlock is visiting this week. |
IFL | KE | KE | |||
| Mon, 13 May 2013 | 1:15-2:45pm, WID room 3160 | Discussion: LL+All | IFL | KE | KE | ||||
| Mon, 20 May 2013 | 1:15-2:45pm, WID room 3160 | Davorka Gulisija | ? |
IFL | KE | KE | |||
| May 27, June 3 2013 |
Break | ||||||||
| Mon, 10 June 2013 | 3:30pm, WID room 3160 | Everybody |
Map out topics for next seminars and present brief update on who does what. | LL | KE | KE |
Group Members and their Research
Our Group is composed of members from a diverse mix of disciplines working on very diverse projects. Here is a brief overview.
| Current Group Members |
Background |
Focus |
|
| Dresler, Jerdon |
undergraduate |
genetics |
start building a model |
| Ehlert, Kurt |
graduate student |
math, neuroscience |
implementing a stochastic simulation algorithm |
| Flores-Lorca, Iratxo | special student | applied math; biochemistry; bio |
making ordinary differential equation solvers accessible |
| Goldstein, Steve |
computational biologist |
probability theory, math, genomics, alignments |
background selection and distributions of mutational effects |
| Keel, Seth |
solutions architect turned graduate student |
computer science; genetics |
computing infrastructure, evolution@home, genetics simulations |
| Kozak, Cassandra |
undergraduate |
biology |
start building a model |
| Loewe, Laurence |
principal investigator |
biology; mol sys bio; theor. population genetics; evolution |
evolutionary systems biology; multi-locus population genetics of mutations; see my research interests |
| Mau, Bob |
biostatistician |
statistics, genomics |
distributions of mutational effects |
| Scheuer, Katherine |
undergraduate | biology | circadian clocks in Drosophila |
| Former Group Members |
|||
| Yang, Payeng |
undergraduate | natural sciences, majoring in biology | parameters of the cholesterol pathway |
| Poon, Philip | postdoc | physics, applied math, numerics | ABC, numerics, simulations of delay |
| Myers, Matt | undergraduate (Summer 2011-2012) |
computer science | implementations in C++, HDF5 |
| Holmes, Peter |
undergraduate Summer 2011 |
math, chem. eng. |
implementing a stochastic simulation algorithm |
Please email the Laurence Loewe if you have any questions about the group, would like to visit or even would like to join the group.
Previous Group Meetings
Group Meetings Fall 2012
| Date | Time+Place | Presenter | Topic |
|---|---|---|---|
| Tue, 18 Sept 2012 |
3:30pm, WID room 3160 | Everybody Discussion |
Map out topics for next seminars and present brief overview on who does what. Discuss next steps towards prototype of evolvix. |
| Tue, 25 Sept 2012 |
3:30pm, WID room 3160 | Laurence Loewe |
Evolvix timeseries review |
| Tue, 2 Oct 2012 | 3:30pm, WID room 3160 | Laurence Loewe | Evolvix Internal Representation |
| Tue, 9 Oct 2012 | 3:30pm, WID room 3160 | Iratxo Flores-Lorca | Timeseries reporting |
| Wed, 10 Oct 2012 | 3:30pm, Genetics Colloquium Biotech |
Jim Faeder |
Rule based modeling |
| Changed to Wed, 17 Oct 2012 |
Changed to 5pm, WID room 3160 |
Payeng Yang |
A model of the cholesterol biosynthesis pathway |
| Tue, 23 Oct 2012 | 3:30pm, WID room 3160 | Laurence Loewe |
Parameter space and other topics |
| Tue, 30 Oct 2012 |
3:30pm, WID room 3160 | Seth Keel |
Introduction to Use-Cases and the population genetics simulator project |
| Tue, 6 Nov 2012 | 3:30pm, WID room 3160 | Laurence Loewe | Group Discussion: How to work with Use Cases |
| Tue, 13 Nov 2012 |
3:30pm, WID room 3160 | Kurt Ehlert |
A new simulation model from work in the lab of Francisco Pelegri |
| Tue, 20 Nov 2012 |
3:30pm, WID room 3160 | Discussion: LL+All |
Work-flow in Evolvix and Use Cases of Parameters |
| Tue, 27 Nov 2012 |
3:30pm, WID room 3160 | Discussion: LL+All | Evolvix: Major Concepts (Table, Field, Record) and format for UserKey data |
| Tue, 4 Dec 2012 | 3:30pm, WID room 3160 | Discussion: LL+All |
Evolvix: Common structures in the syntax of KeyConcepts. |
| Tue, 11 Dec 2012 | 3:30pm, WID room 3160 | Kate Scheuer | Circadian clocks: Contrasting two models. |
| Thur, 13 Dec 2012 |
7pm, WID, room 3245 |
Everybody |
Holiday party: Start about 7, please let Iratxo know what Pizza/Salad/etc you want to order. |
| Tue, 18 Dec 2012 | 4pm WID room 3160 | Bob Mau | Measuring DNA sequence diversity for population genetics purposes |
| break | |||
| Tue, 15 Jan 2013 | 3:30pm, WID room 3160 | Everybody |
Map out topics for next seminars and present brief overview on who does what. |
Group Meetings Summer 2012
| Date | Time+Place | Presenter | Topic |
|---|---|---|---|
| Fri, 25 May 2012 |
3:30pm, WID room 3130 | Philip Poon | Join WID Very Informal Seminar Series for presentation by Philip Poon. |
| Fri, 1 June 2012 |
3:40pm, WID room 3160 | Laurence Loewe |
Open discussion on how to organize group meetings and other things in group life |
| Fri, 8 June 2012 | 9am-4pm The Pyle Center, 702 Langdon Street |
http://www.gstp.wisc.edu/ | Annual Retreat for Genomic Sciences Trainings Program |
| Fri, 15 June 2012 | 3:30pm, WID room 3130 | Pupa Gilbert (physics) | Join WID Very Informal Seminar Series |
| Tue, 19 June 2012 | 3:30pm, WID room 3160 | Davorka Gulisija |
Population genetics of fluctuating selection |
| Fri, 29 June 2012 |
3:40pm, WID room 3160 | Laurence Loewe, Seth Keel |
GIT |
| Tue, 3 July 2012 | 3:30pm, WID room 3160 | Seth Keel | VSV Simulation or Data Infrastructure |
| Fri, 13 July 2012 |
3:40pm, WID room 3130 | Sushmita Roy |
Join WID Very Informal Seminar Series for presentation by Sushmita Roy. |
| Thu, 19 July 2012 | 1-5pm, TBA | please all come |
Joint Madison Labs Population Genetics Meeting |
| Tue, 24 July 2012 |
3:30pm, WID room 3160 | Philip Poon, Laurence Loewe |
Preview Talks on EvoSysBio Meeting |
| Mon 30 July-Wed 1 August |
3rd Floor Teaching Lab, WID |
Bigger event organized by our group with many talks over 3 days. Please all come. | EvoSysBio meeting |
| break |
no meeting |
||
| Tue, 21 August 2012 | 3:30pm |
CMake, code merging, etc discussions |
Special Discussion with Seth, Kurt, Iratxo and Laurence |
| Tue, 28 August 2012 | 3:30pm, WID room 3160 | Iratxo Flores-Lorca | How to record timeseries |
Group Meetings Spring 2012
| Date | Time + Place |
Presenter | Topic |
|---|---|---|---|
| Fri, 10 Feb 2012 |
TownCenter, WID |
Darwin Day |
A celebration of the diversity in biology. |
| Fri, 17 Feb 2012 | 3:40pm, WID room 3160 | Laurence Loewe |
NFsim: Rule-based modelling for systems biology |
| Wed, 22 Feb 2012 | 3:30pm Genetics Colloquium | Sushmita Roy |
Reconstruction and analysis of evolution of condition-specific transcriptional programs |
| Fri, 24 Feb 2012 | 3:40pm, WID room 3160 | Laurence Loewe |
Naming contest for basic concepts of simulation |
| Fri, 2 Mar 2012 | 3:40pm, WID room 3160 | Everybody |
What everybody is working on + Open discussion: How does it all fit together? |
| Fri, 9 Mar 2012 | 3:40pm, WID room 3160 | Kurt Ehlert |
Stochastic simulations via the Sorting Direct Method |
| Fri, 16 Mar 2012 | 3:40pm, WID SysBio Cone |
Laurence Loewe |
Very informal seminar series: How to store simulation data |
| Fri, 23 Mar 2012 | 3:40pm, WID room 3160 | Philip Poon |
Stochastic simulations via the Next Reaction Method |
| Fri, 30 Mar 2012 | 3:40pm, WID room 3160 | Katie Scheuer |
Drosophila Clock |
| Mini-break |
- |
- |
- |
| Wed, 18 Apr 2012 |
UW-Madison | Undergraduate symposium |
|
| Fri, 20 Apr 2012 | 3:40pm, WID room 3160 | Iratxo Flores-Lorca | Solvers for differential equations |
| Fri, 27 Apr 2012 | 3:40pm, WID room 3160 | Bob Mau |
Measuring DNA Sequence Diversity |
| Mini-break | - |
- |
- |
| Fri, 11 May 2012 | 3:30pm, 168 Noland Hall, cookies from 3:10pm in room 163 |
Nipam Patel (http://www.patellab.org/) |
Bio Colloquium: Evolution of Development of Arthropod Body Patterning |
| Fri, 18 May 2012 | 3:40pm, WID room 3160 | Bob Mau | Estimating Distributions of Mutational Effects from Diversity |
Group Meetings Fall 2011
| Date | Time + Place |
Presenter | Topic |
|---|---|---|---|
| 29-30 Sept 2011 |
Whole day, WID |
MathBio3 | Conference on Mathematical Modelling in Biology. Please go there as much as you can. See weblink. |
| Thur, 13 Oct 2011 |
1:30pm, WID room 3160 | Bob Mau |
Comparative genomics of pathogenic bacteria |
| Wed, 19 Oct 2011 | 12pm, WID room 3160 |
Laurence Loewe |
Challenges in antibiotics resistance evolution |
| Wed, 2 Nov 2011 |
3:30pm Genetics Colloquium | Michael Lynch (Bloomington, IN) |
Mutation and Evolution (Host: L Loewe) |
| Thur, 3 Nov 2011 | 12pm Evolution Seminar Series | Michael Lynch (Bloomington, IN) | The causes and consequences of meiosis suppression in Daphnia (Host: L Loewe) |
| Fri, 4 Nov 2011 |
2:30pm, WID room 3160 | Payeng Yang |
Parameters in the cholesterol biosynthesis pathway |
| Wed, 9 Nov 2011 | 12pm, WID room 3160 | Katie Scheuer | The circadian clock of Drosophila |
| Thur, 10 Nov 2011 |
2:25pm Van Vleck Hall, room 901 |
David Anderson (UW-Madison, Math) |
[Probability seminar] Highly recommended for all maths/simulation researchers |
| Wed, 16 Nov 2011 | 12pm, WID room 3160 | Philip Poon |
Thoughts on Approximate Bayesian Computation |
| DateChange: Tue, 22 Nov 2011 |
TimeChange: 4pm, WID room 3160 |
Seth Keel and Matt Myers |
How to handle code effectively using version control, issue tracking and other tools. |
| Wed, 30 Nov 2011 | 12pm, WID room 3160 | Group discussion |
How to handle code effectively using version control, issue tracking and other tools. |
| DateChange: Tue, 6 Dec 2011 |
TimeChange: 4pm, Biotechnology Center Auditorium |
David J. Baumler (UW-Madison, Genome Center of Wisconsin) |
[CIBM Seminar] Investigating Modern-Day Disease by Using Metabolic Models of Bacteria from the Past |
| Wed, 7 Dec 2011 |
4pm 140 Bardeen, Statistics |
David Anderson (UW-Madison, Math) | [Statistics seminar] Highly recommended for all maths/simulation researchers |
| Wed, 14 Dec 2011 | TimeChange: 12:30pm, WID room 3160 | Iratxo Flores-Lorca |
Informal chat about the ODE solver CVODEs. Not for biologists (at least not for now). |
| Wed, 21 Dec 2011 | 12pm? WID room 3160 | Laurence Loewe |
Next Reaction Method. |
