Algebraic Biology at Cass 2012 - ABaCass2012 (=A(lgebraic)B(iology)a(t)CASS)2012

Algebraic Biology Workshop in the Southern Alps

Saturday 4th February - Friday 10th February, 2012

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Cass Field Station
Arthur's Pass
Southern Alps
New Zealand

Workshop co-ordinator:

Raazesh Sainudiin
Mathematics and Statistics Department
University of Canterbury
Private Bag 4800
Christchurch 8041
Phone: +64 3 364 2987 extn 7682 (ext 7691)
Fax: +64 3 364 2587

Photograph Galley page from Cass workshop 2009.


2009 This meeting is by invitation only (if interested contact Raazesh Sainudiin)

The objective of ABaCass2012 is to facilitate uninterrupted and balanced Face-to-Face Transmissions in Contemporary Algebraic Biology, where Algebraic Biology is nothing more than algebraically flavoured mathematical communications in biology!

Besides your laptop, bring plenty of paper, pens, and ideas. Also bring some hiking shoes/jacket. Be prepared to do your own cooking (there are no shops or cafes nearby). There is little (if any) phone or internet access. There is no charge for invited participants, but you may wish to bring along some of your own food, particularly if you have a special diet (eg. vegan), and some refreshments.

Funding from the NZ Marsden Fund and Allan Wilson Centre.

Information for participants:

There are a few tutorials to provide some structure for the exchange of ideas. Each tutorial has two parts and each part is about 1.5 hours long with a thinking/hiking/eating/relaxing break of at least 4 hours between most tutorial pairs.

  1. Saturday 4th February 2012, Raazesh Sainudiin, Department of Mathematics and Statistics, University of Canterbury, NZ
    • (part 1) Controlled Lumped Coalescent Processes for Population Genomic Inference (recast of (PDF 2.9MB))
    • Background Papers:
      • Experiments with the Site Frequency Spectrum, Raazesh Sainudiin, Kevin Thornton, Jennifer Harlow, James Booth, Michael Stillman, Ruriko Yoshida, Robert Griffiths, Gilean McVean and Peter Donnelly, Bulletin of Mathematical Biology, Volume 73, Number 4, 829-872, 2011 (AMS review)
      • A unified multi-resolution coalescent: Markov lumpings of the Kingman-Tajima n-coalescent, Robert Griffiths, Raazesh Sainudiin and Tanja Stadler -- UCDMS Research Report 2009/4, April 5, 2009 (PDF 692KB)
  2. Sunday 5th February 2012, Jeremy Sumner, School of Mathematics and Physics, University of Tasmania, Australia
    • (part 1) The intertwining algebra of Markov process and phylogenetic branching
    • (part 2) Applications of the intertwining algebra of Markov process and phylogenetic branching
    • Mareike Fischer notes for both parts (PDF 408KB)
    • Background Papers:
      • The algebra of the general Markov model on phylogenetic trees and networks arXiv
      • A tensorial approach to Hadamard-type inversion of Abelian group-based models (email Jeremy for current draft)
  3. Monday 6th February 2012, Mike Steel, Department of Mathematics and Statistics, University of Canterbury, NZ
    • (part 1) Phylogenetic diversity over an Abelian group
    • (part 2) Phylogenetic theory for non-Abelian group dissimilarities
    • Mike Steel's notes for both parts up-side-down! (PDF 592KB)
    • Background Papers:
      • Dress, A. and Steel, M. (2007). Phylogenetic diversity over an abelian group Annals of Combinatorics 11, 143-160. PDF
      • Bandelt, H.-J. and Steel, M.A. (1995). Symmetric matrices representable by weighted trees over a cancellative abelian monoid. SIAM Journal on Discrete Mathematics 8(4): 517-525. PDF
      • Semple, C. and Steel, M.A. (1999). Tree representations of non-symmetric, group-valued proximities. Advances in Applied Mathematics 23: 300-321.PDF
  4. Tuesday 7th February 2012, Megan Owen, Fields Institute, Toronto, Canada
    • (part 1) Polynomial time geodesic distance algorithms (PDF 536KB)
    • (part 2) Statistical Implications of polynomial time geodesic distance algorithms
    • Background Papers:
      • L. Billera, S. Holmes, K. Vogtmann. Geometry of the space of phylogenetic trees preprint
      • M. Owen, J.S. Provan. A fast algorithm for computing geodesic distances in tree space arXiv
  5. Wednesday 8th February 2012, Group Hiking Day, guided by Jennifer Harlow of Christchurch Tramping Club
    • Plan A: Mt Bealey.
      [This would be suitable for fit people with tramping experience.]
      "The tramp climbs steeply through beech forest on a well defined track to continue climbing (above the bushline) on a tussock and rock ridge. Mt Bealey itself is 1836m high, which means a total ascent of about 1100m, some of it steep. Stunning views on a clear day."
    • Plan B: Bealey Spur
      [IF (the group cannot do Mt Bealey) OR (does not want to do Mt Bealey) OR (the weather is bad AND subgroup still wants to go somewhere)]
      "Start above the baches at Bealey Spur and climb up through sheltering beech forest. On the way to the charming old hut, at about 1240m, the ridge opens up in places to reveal immense views over the Waimakariri River and to the mountains beyond. The hut is about a 450m climb from the cars and the round trip is about 10km. Option to continue up Hut Spur above the bushline for a bit to admire the impressive horseshoe ridge."
  6. Thursday 9th February 2012, Terrell Hodge, Associate Dean, College of Arts and Sciences, Western Michigan University, Kalamazoo, USA
    • (part 1) Some Modern Discrete Mathematical Approaches to Metabolic Pathways (elementary graph and linear algebraic approaches)
    • (part 2) Metabolic Pathways: Some Algebraic Approaches (towards possibilities for employing quivers, hypergraphs, and related algebras)
    • Background and Introduction:
      • Mathematical concepts and methods in modern biology: using modern discrete models. R. Robeva and T. Hodge, editors, Elsevier Press, 2012.
  7. Friday 10th February 2012, Raazesh Sainudiin, Department of Mathematics and Statistics, University of Canterbury, NZ
    • (part 2) Randomised algorithms over dense trees of trees for massive metric data streams (recast of (PDF 7.2MB)) and their possible extensions to CAT(0) tree spaces
    • Background Papers:
      • Posterior expectation of regularly paved random histograms, Gloria Teng, Jennifer Harlow, Dominic Lee and Raazesh Sainudiin, October 30, 2011 ... Friday 13 January 2012 (PDF 433KB)
      • Statistical regular pavings to analyze massive data of aircraft trajectories, Gloria Teng, Kenneth Kuhn and Raazesh Sainudiin, Journal of Aerospace Computing, Information and Communication, February 7, 2012 (PDF 4.8MB)
  8. Friday 10th February 2012, Pack-up, Clean-up and Leave after lunch!

Confirmed Participants: Joshua Collins, Mareike Fischer, Terrell Hodge, Leo van Iersel, Stefan Grunewald, Steffen Klaere, Iain Martyn, Megan Owen, Raazesh Sainudiin, Scott Schmidler, Mike Steel, Jeremy Sumner.

Transportation Logistics to Erskine Carpark at 10:00AM on Saturday February 4 2012 NZST: Gabriela Aguileta (independent arrangement to Cass but never showed up) Joshua Collins (independently came to Erskine carpark), Mareike Fischer (5 minute walk to Erskine carpark), Terrell Hodge (pick-up by Stefan Grunewald), Leo van Iersel (pick-up by Steffen Klaere), Stefan Grunewald (driver), Steffen Klaere (driver), Iain Martyn (Meet at Erskine Carpark by 10:00AM and independent arrangement to Cass), Megan Owen (5 minute walk to Erskine carpark; Mareike Fischer assisted), Raazesh Sainudiin (driver), Scott Schmidler (5 minute walk to Erskine carpark), Mike Steel (driver), Jeremy Sumner (pick-up by Stefan Grunewald).

Food - We cook and clean in groups to have dinner together around 1800 hours or so each day (details to be mutually agreed after lunch on Saturday).
Toward this please read Mailee Stanbury's instructions to the Tenzo! (PDF) (ingredients (PDF) :: Grogery List 1 (PDF) + Grocery List 2 (TXT) + Grocery List 3 (TXT)).
Make your own breakfast [cereal, muesli, milk from powder, eggs and potatos, juice, toast, spreads, tea, coffee] and lunch [sandwiches with meat, cheese and/or filafel (only for strict vegetarians) with vegetables]. All these ingredients are provided.

Locally Recommended Hikes - (You may not take off on your own! Talk to Raaz first.) Some options given that time frame, and depending on weather, fitness etc could include::

  • Straightforward options:
    • climbing up Sugarloaf (the obvious steep hill behind the field station) [near Cass]
    • walk up Bealey Spur to hut and beyond [near Cass]
    • walk up Otira valley (or Bealey valley), or Sudden valley [near Cass]
    • Explore Castle Hill limestone area and walk through Cave stream [near Cass]
    • Climb Avalanche peak [Arthurs Pass]
  • Trips requiring some navigation/rock scrambling/fitness/head for heights:
    • Traverse of Mt Binser [near Cass]
    • Climb Mt Bealey, descent via Rough Creek
    • Avalanche peak traverse to Mt Bealey, descent via Rough Creek
    • Up Otira valley and onto Goldney Ridge (with option of low peak of Mt Rolleston)
    • West ridge Mt Phipps, or Rome Ridge (but not to summits)

Previous Cass Workshops

  • Cass09 - Wild ideas: speculations in theoretical evolutionary biology
  • Cass07 - Random models in phylogenetics and resolving ancient divergences
  • Cass06 - Random models in phylogenetics and resolving ancient divergences

Photograph Galley page from previous Cass workshops.

Group photo from 2009 Accommodation:

Cass Field Station has bunkrooms. Please bring a sleeping bag and pillowcase. More information is available on the Cass Field Station website.

Getting there:

Information on how to get there can be found on the Cass Field station website. We will be taking a minivan up to Cass. Please let us know if you need transport.


Raazesh Sainudiin thanks Ms. Penelope Goode for a most efficient administrative support and Ruriko Yoshida for setting this meeting in motion despite her inability to be there.

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Last modified on Saturday, 03-Sep-2016 04:25:43 MST and served on Sunday, 25-Jun-2017 13:45:59 MST.

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