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Evolutionary Systems Biology Group - Homepage

Brief group overview and relevant pointers for now. A new lab website is under construction.

This is a temporary part of the homepage of the Evolutionary Systems Biology Group at the University of Wisconsin-Madison. It gives a brief overview of group members and some other group info.

 

Lab Group Meetings 2015

There are different types of lab meetings which are held as needed. Due to the broad interdisciplinary nature of the group, different meetings often have different sets of participants. Please email Laurence Loewe, if you would like to visit and/or present something at any of these meetings:

  • Office hours: upon request, please email Laurence Loewe at his wisc address.
  • SysBio: coordinating work towards an integrated molecular systems biology models of the circadian clock in Drosophila melanogaster.
  • PopGen: exploring questions on how to estimate diversity, quantify background selection and selective sweeps.
  • Math: exploring math questions about parameter estimation, optimization, and simulation algorithms.
  • Evolvix developer: coordinating work towards implementing Evolvix on the more practical side, for those design ideas that are ready to be put in code.
  • Evolvix system design: exploring how to find, evaluate, and select/reject ideas about how Evolvix as a computational system should be implemented to make it easy to maintain backwards compatibility, semantic stability, efficiency of development, numerical/semantic accuracy, computational speed and excellent usability, without making it impossible to implement.
  • Evolvix syntax and semantics: exploring how Evolvix should or could look like as a formal language by brainstorming ideas and testing them as follows. Visitors are welcome to join us in this and we might arrange special meetings if you are interested in any of the following and can help us to meet a corresponding need in Evolvix by:
    • evaluating syntax to maximize simplicity (we always need biology undergraduates who can tell us what they understand and what they don't; let us know if you are interested) while also
    • maximizing semantic and technical accuracy (we also need experts who are competent reviewers with a deep understanding of the semantics of their domain and can accept/reject proposed names as reasonable choices for the semantics to be implemented; let us know if you are interested in such discussions, which can be either one-off or more frequent, as needed).
    • hanging in the balance until we can meet the challenge to do both (timing can be hard to predict):
      • find words that are easy to understand (if not, undergrads get veto-rights by the lead designer to avoid obfuscating meaning in Evolvix by the jargon, cryptic symbols and historical contingencies that many experts wrongly think are easy).
      • find words that are judged to be semantically rigorous and not misleading (else experts get veto-rights by the lead designer to keep undergrads from importing semantic confusion into the core of the language).
      • documenting our choices, alternatives and rejections along the way with reasons for our decisions (to minimizing repeating these discussions...)
    • celebrating once we found words worthy of making it into the language (often after reworking core concepts in ways that experts find intriguing). We had enough surprising successes to justify the time it takes to use this way of translating between the accuracy of math and the intuition of biologists. These meetings do more to break down the dreaded math-bio language barrier than many other approaches; hence it is worth investing in these open-ended discussions.
  • Management: how to better organize and facilitate Evolvix development and lab life

 

Interactive writing support

Are you a student at UW-Madison, a native English speaker, good at explaining things, and interested in watching a scientific paper develop, while simultaneously contributing towards improving the clarity of the presentation? If yes, then you might be interested in trying how it is for you to provide what could be called 'interactive writing support'. While there is no need for you to know anything about science, interactive writing support is an excellent opportunity to learn a lot about about the field that the paper contributes to, or about how some types of scientific papers are written. Interactive writing support is a new idea (as far as we know), which is currently under development in our lab. While this probably doesn't work for everybody, it might be something you would be interested in.  Please email Laurence Loewe, if you would like to discuss this. 

 

 

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
Loewe, Laurence principal investigator evolution, pop gen, mol sys bio; evosysbio, modeling, compiler design
evolutionary systems biology of clocks; multi-locus population genetics of mutations; fitness landscapes; ABC; CTMCs; see my research interests
Keel, Seth solutions architect, project manager and more
computer science, genetics, project management, systems design
project management, build systems, distributed computing infrastructure, Muller's ratchet, evolution@home, population genetics simulations, ABC, C++
Ehlert, Kurt
graduate in training, will go to math math, neuroscience, genetics, computing, and more math
stochastic simulation algorithms, parameter estimation, Approximate Bayesian Computation, Time series storage, build system, C++ and more
Engbretson, Tanner
graduate in training
computer science
web graphical user interface for Evolvix, plotting, JavaScript, node server, human computer interfaces and more.
Vaibhav Vyas
project assistant
computer science, NVidia
boost multi-precision numbers, boost math, how to call c++ functions from Evolvix
Dinesh Thangavel
project assistant computer science data structures for storing names and sequences in Evolvix.
Scheuer, Katherine graduate in training biology / Spanish / psychology
modeling circadian clocks in Drosophila; Evolvix syntax review for ease of use and biological semantics; Evolvix outreach
Alyssa Hotz
undergraduate biology contributions to modeling the circadian clock in Drosophila
Erik Nolen
undergraduate biology contributions to modeling the circadian clock in Drosophila
Devanie Tucker
undergraduate biology contributions to modeling the circadian clock in Drosophila
Jerdon Dresel
undergraduate biology contributions to modeling the circadian clock in Drosophila








Former Group Members


Mau, Bob biostatistician statistics, genomics estimating measures of DNA sequence diversity
Flores-Lorca, Iratxo graduate in training applied math; bioinformatics efficient time-series recording and ordinary differential equation solver integration in Evolvix
Goldstein, Steve computational biologist probability theory, math, genomics, alignments inference of selection from next-gen sequencing data in Drosophila
Goldfinger, Jacob undergraduate biology, math tutorials for first steps in Evolvix
Dresler, Jerdon undergraduate genetics aspects of a circadian clock model in Drosophila
Kozak, Cassandra undergraduate biology aspects of documenting an Evolvix model of the cholesterol pathway
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++, early HDF5 experiments
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 think about joining the group.

 

 

 

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