Seminar Computational Life Science

Seminar Computational Life Science

Students will be able to independently develop the contents of scientific publications from at least two different fields of Computational Modelling and Simulation and present them to third parties in a comprehensible manner, and critically analyse the acquired knowledge. They are able to critically analyse and communicate the application of computational modelling methods in two different application areas and to recognise cross-application approaches.


Contents

Analysis and discussion of scientific publications on a topic of the student's choice in the fields of Computational Life Sciences.


Program / Module

M.Sc. Computational Modeling and Simulation
Module: CMS-SEM - Literature Review in Computational Modelling


Time/Place
Summer Term

Seminar: Tuesdays, 13:00-14:30h


SEMINAR STARTS APRIL 7 AND IS HELD ENTIRELY ONLINE THIS SEMESTER. It will be held as Zoom live screen-casts with the possibility to ask questions. Links will be announced here below. In order to keep this as close as possible to a real lecture experience, and to allow interactive student presentations, the webcasts are not recorded.

Format

2 SWS seminar, self-study

2,5 credits


Exam

Oral presentation ("Referat") of 30 minutes (20 mins talk + 10 mins Q+A).
Registration for the exam via SELMA before April 27. Students who are not registered for the exam are not allowed to present in the seminar.


Grade scale:

Grading of the seminar is strict according to general expectations in industry and academia for such presentations and using the following criteria:

  • quality of presentation / presentation style
  • quality and correctness of contents
  • technical depth and level of understanding conferred
  • understandability
  • response to questions
  • bigger picture, context, own critical analysis and discussion of results
The following guideline is used for grading:
  • Grade 1: Outstanding presentation, both in contents and quality. Significantly goes beyond the very paper discussed, also presenting the context, big picture, and discussing impact over time.
  • Grade 2: Good presentation which teaches at least one core concept from computational modeling and simulation in the life sciences in a didactic and understandable way.
  • Grade 3: Average presentation according to expectations that discusses the paper and its context, but neither teaches anything new, nor gives the bigger picture and analysis of the work.
  • Grade 4: Minimal requirements met, but presentation quality and/or contents below expectations.
  • Grade 5: Failed. No-show, or even core concepts of the presented paper were not presented or understood.
For gradation, individual grades can be lowered or raised by 0.3 points (e.g., 2.7 = better than average, but not quite good). The grades 0.7, 4.3, and 4.7 are not to be used (see exam regulations). All grades above 4.1 are equivalent to a 5.


Exam Review

You have the opportunity to receive feedback on your performance and discuss it in an online exam review session

on Sept 21, 2020, at 9am.

https://us02web.zoom.us/j/82083582747?pwd=OW5FSHQwVnRKbU13NjhhN0dFYTUvdz09

Meeting ID: 820 8358 2747

Passcode: 243428

Participants will be let in one by one in the order of arrival. There is a waiting room for you to log in to until it is your turn.


Registration to the course

For students of the Master program "Computational Modeling and Simulation: via CampusNet SELMA.
Registration deadline: April 14, 2020. Late registrations cannot be accepted.


Teachers

Lecture: Prof. Ivo F. Sbalzarini

Teaching language: ENGLISH


Seminar Papers

Click here to see the list of suggested seminar papers to choose from
PLEASE CHECK THE SCHEDULE BELOW AND INFORM ME OF ERRORS. The schedule is final, no changes are possible any longer.


Seminar Schedule
  • April 7: Seminar introduction and assignment of topics. ALL STUDENTS WHO INTEND TO PRESENT IN THIS SEMINAR MUST BE PRESENT IN ORDER TO RECEIVE A TOPIC. (Webcast link: https://zoom.us/j/810222791?pwd=dCtiODh6Z21WTS9FMG5laDc2VW9WQT09, Meeting ID: 810 222 791, Password: 071006)

  • April 14: Q+A of papers, review of assignments, seminar schedule, registration and examination details. (Webcast link: https://zoom.us/j/614893564?pwd=ckhhMkR5OGpOVWdTWVNDcHkzQTJNQT09, Meeting ID: 614 893 564, Password: 076169)

  • April 28:

    Webcast link: https://zoom.us/j/91008957036?pwd=QVo0QVFvR0VRZWhGNS9MdEVvT0FPdz09, Meeting ID: 910 0895 7036, Password: 059389.


    Eric Darve, David Rodríguez-Gómez, and Andrew Pohorille. Adaptive biasing force method for scalar and vector free energy calculations. J. Chem. Phys., 128(14):144120, 2008.
    — Chetan Munegowda

    Data-analysis strategies for image-based cell profiling. JC Caicedo, S Cooper, F Heigwer, S Warchal, P Qiu, C Molnar, ... Nature methods 14 (9), 849.
    — Shivangi Singh

    Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. E Meijering, M Jacob, JCF Sarria, P Steiner, H Hirling, M Unser. Cytometry Part A: the journal of the International Society for Analytical …
    — Kenza Garreau

  • May 5:

    Webcast link: https://us02web.zoom.us/j/84959099837?pwd=ZnVJRGllM0FFbUQ4OE05L25nRVFNQT09, Meeting ID: 849 5909 9837, Password: 155899.


    Basic local alignment search tool. SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman. Journal of molecular biology 215 (3), 403-410.
    — Stefano Fogarollo

    Jean-Christophe Olivo-Marin, Extraction of spots in biological images using multiscale products, Pattern Recognition, Volume 35, Issue 9, September 2002, Pages 1989-1996.
    — Ananya A Bejai​

    Robustness in bacterial chemotaxis. U Alon, MG Surette, N Barkai, S Leibler. Nature 397 (6715), 168-171.
    — Rushikesh Shinde

  • May 12:

    Webcast link: https://us02web.zoom.us/j/87193333894?pwd=UUwzK1VnNUE2MUQyN1FLV01Fc0RoZz09, Meeting ID: 871 9333 3894, Password: 862946.


    Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. B Zagrovic, CD Snow, MR Shirts, VS Pande. Journal of molecular biology 323 (5), 927-937.
    — Philipp Schake

    Exact stochastic simulation of coupled chemical reactions. DT Gillespie. The journal of physical chemistry 81 (25), 2340-2361.
    — Omar Faruk

    F. Ghesu et al., "Multi-Scale Deep Reinforcement Learning for Real-Time 3D-Landmark Detection in CT Scans," in IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 1, pp. 176-189, 1 Jan. 2019.
    — Chethan Babu Venkata Reddy

  • May 19:

    Webcast link: https://us02web.zoom.us/j/83803905505?pwd=VDFVN3VPUnRqczl5UGpRUW5nTjRnUT09, Meeting ID: 838 0390 5505, Password: 250003.


    Collective Langevin dynamics of flexible cytoskeletal fibers. Nedelec, Francois and Foethke, Dietrich. New Journal of Physics 9(11):427, 2007.
    — Sadika Tanzila

    An auxin-driven polarized transport model for phyllotaxis. H Jönsson, MG Heisler, BE Shapiro, EM Meyerowitz, E Mjolsness. Proceedings of the National Academy of Sciences of the United States of America, 2006.
    — Niranjan Niranjan Manur Krishnamurthy

    Entropic effects in cell lineage tree packings. JI Alsous, P Villoutreix, N Stoop, SY Shvartsman, J Dunkel. Nature physics 14 (10), 1016-1021, 2018.
    — Charvi Jain

  • May 26:

    Webcast link: https://us02web.zoom.us/j/86003817860?pwd=T1JaaGc1RlB1cFFuZWM0OHpGVkZydz09, Meeting ID: 860 0381 7860, Password: 053463.


    Garnier J, Osguthorpe DJ, Robson B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 120:97-120.
    — Yana Vassileva

    CANCELED Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. JA Helmuth, G Paul, IF Sbalzarini. BMC bioinformatics 11 (1), 372.
    — Mounika Kommi

    H. I. Saleheen and K. T. Ng. New finite difference formulations for general inhomogeneous anisotropic bioelectric problems. IEEE Trans. Biomed. Eng., 44(9):800–809, 1997.
    — Ashiah Kangen

  • Jun 9:

    Webcast link: https://us02web.zoom.us/j/83862090384?pwd=aWVnNTF1STdQdWJ5dlR5YVAyNWwydz09, Meeting ID: 838 6209 0384, Password: 533807.


    Simulation of stochastic reaction-diffusion processes on unstructured meshes. S Engblom, L Ferm, A Hellander, P Lötstedt. SIAM Journal on Scientific Computing 31 (3), 1774-1797.
    — Philipp Suhrcke

    Optimization of mutual information for multiresolution image registration. P Thévenaz, M Unser. IEEE transactions on image processing 9 (12), 2083-2099.
    — Zaki Imam

    A predictive 3D multi-scale model of biliary fluid dynamics in the liver lobule. K Meyer, O Ostrenko, G Bourantas, H Morales-Navarrete, N Porat-Shliom, ... Cell systems 4 (3), 277-290. e9.
    — Maksim Zhdanov

  • Jun 16:

    Webcast link: https://us02web.zoom.us/j/82713864863?pwd=VXVCcnVTVnk5bzhFK2lHS1lvYi85dz09, Meeting ID: 827 1386 4863, Password: 024234.


    A computational clonal analysis of the developing mouse limb bud. L Marcon, CG Arqués, MS Torres, J Sharpe. PLoS computational biology 7 (2), e1001071.
    — Kaustav Das

    F. Raynaud, M. E. Ambühl, C. Gabella, A. Bornert, I. F. Sbalzarini, J.-J. Meister, and A. B. Verkhovsky. Minimal model for spontaneous cell polarization and edge activity in oscillating, rotating and migrating cells. Nature Physics, 12:367–373, 2016.
    — Serhii Yaskovets

    T. J. English and D. A. Hammer. The effect of cellular receptor diffusion on receptor-mediated viral binding using Brownian adhesive dynamics (BRAD) simulations. Biophys. J., 88:1666–1675, 2005.
    — Qing Cao

  • Jun 23:

    Webcast link: https://us02web.zoom.us/j/87959690046?pwd=bXRPcSs5eTBhMGo3bGp1eS9TK3N2dz09, Meeting ID: 879 5969 0046, Password: 302890.


    Chen L., Strauch M., Merhof D. (2019) Instance Segmentation of Biomedical Images with an Object-Aware Embedding Learned with Local Constraints. In: Shen D. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2019. MICCAI 2019. Lecture Notes in Computer Science, vol 11764. Springer, Cham
    — Prafful Pawar

    Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. U Alon, N Barkai, DA Notterman, K Gish, S Ybarra, D Mack, AJ Levine. Proceedings of the National Academy of Sciences 96 (12), 6745-6750.
    — Jyotirmaya Ijaradar

    Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. J Paulsson, OG Berg, M Ehrenberg. Proceedings of the National Academy of Sciences 97 (13), 7148-7153.
    — Hanna Wiederanders

  • Jun 30:

    Webcast link: https://us02web.zoom.us/j/84080078291?pwd=QUFhQzZuNDROZ25QVWNlbGZmUVlZUT09, Meeting ID: 840 8007 8291, Password: 837701.


    A mechanism for cell motility by active polar gels. W Marth, S Praetorius, A Voigt. Journal of The Royal Society Interface 12 (107), 20150161.
    — Nilakantha Sahoo

    Asymmetric division coordinates collective cell migration in angiogenesis. G Costa, KI Harrington, HE Lovegrove, DJ Page, S Chakravartula, ... Nature cell biology 18 (12), 1292.
    — Aaron Arellano

    CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. M Held, MHA Schmitz, B Fischer, T Walter, B Neumann, MH Olma, ... Nature methods 7 (9), 747.
    — Vincent Markert

  • Jul 7:

    Webcast link: https://us02web.zoom.us/j/81170618511?pwd=SkFNNDJBci9hMmV1dTluaVJMZmdHdz09, Meeting ID: 811 7061 8511, Password: 342677.


    M. A. Gibson and J. Bruck. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A, 104:1876–1889, 2000.
    — Alisa Mironenko

    Tracking single particles and elongated filaments with nanometer precision. F Ruhnow, D Zwicker, S Diez. Biophysical journal 100 (11), 2820-2828.
    — Barkur Dharshan

    Parameter inference for stochastic single-cell dynamics from lineage tree data. Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner and Mustafa Khammash. BMC Systems Biology, vol. 11, pp. 52, BioMed Central, 2017.
    — Lalith M.

  • Jul 14:

    Webcast link: https://us02web.zoom.us/j/84025173585?pwd=MGRMVEVRdE9keGR1USt6MjRUQTludz09, Meeting ID: 840 2517 3585, Password: 765787.


    M. J. Saxton. Anomalous subdiffusion in fluorescence photobleaching recovery: a Monte Carlo study. Biophys. J., 81:2226–2240, 2001.
    — Gesine Müller

    Bruce E. Shapiro and Eric Mjolsness. “Pycellerator: An arrow-based reaction-like modelling language for biological simulations”. Bioinformatics, Oct 26. 2015. DOI: 10.1093/bioinformatics/btv596.
    — Md Tarekul Islam

    Real-time computing without stable states: A new framework for neural computation based on perturbations. W Maass, T Natschläger, H Markram. Neural computation 14 (11), 2531-2560.
    — Nazia Afrin

  • Jul 21:

    Webcast link: https://us02web.zoom.us/j/84901700306?pwd=WnBCSnZ5KzdvS2ZDNTk1cW5Xendldz09, Meeting ID: 849 0170 0306, Password: 451935.


    Large-scale computation of elementary flux modes with bit pattern trees. M Terzer, J Stelling. Bioinformatics 24 (19), 2229-2235.
    — Synchon Mandal

    J. Cardinale, G. Paul, and I. F. Sbalzarini. Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process., 21(8):3531–3545, 2012.
    — Florian Schier

    Modeling the heart--from genes to cells to the whole organ. D Noble. Science 295 (5560), 1678-1682.
    — Sunny Raghav

  • Jul 28:

    Webcast link: https://us02web.zoom.us/j/83253953320?pwd=Q3VJRXkyVzdLeUR1SXk3dVdSY3UwZz09, Meeting ID: 832 5395 3320, Password: 503868.


    A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. DP Tieleman, SJ Marrink, HJC Berendsen. Biochimica et Biophysica Acta (BBA)-Reviews on Biomembranes 1331 (3), 235-270.
    — Subasini Thangamani

    Ryser, Marc D, et al. “Mathematical Modeling of Spatio-Temporal Dynamics of a Single Bone Multicellular Unit.” Journal of Bone and Mineral Research, vol. 24, no. 5, 2009, pp. 860–870., doi:10.1359/jbmr.081229.
    — Katie Brown

    Robust classification of protein variation using structural modelling and large-scale data integration. EH Baugh, R Simmons-Edler, CL Müller, RF Alford, N Volfovsky, AE Lash, ... Nucleic acids research 44 (6), 2501-2513, 2016.
    — Alexander Shmelkin

  • Aug 4:

    Webcast link: https://us02web.zoom.us/j/86335989440?pwd=blVEc0JvMitsTGdUbEtCcFN2OW5LZz09, Meeting ID: 863 3598 9440, Password: 078819.


    Lespinats S, Grando D, Maréchal E, Hakimi MA, Tenaillon O, Bastien O (2011). "How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling". Evolutionary Bioinformatics Online. 7: 61–85.
    — Jessica Andrade

    Coupling image restoration and segmentation: a generalized linear model/Bregman perspective. G Paul, J Cardinale, IF Sbalzarini. International journal of computer vision 104 (1), 69-93.
    — Israt Jahan Tulin

    Robustness of cellular functions. J Stelling, U Sauer, Z Szallasi, FJ Doyle III, J Doyle. Cell 118 (6), 675-685.
    — Soumyadeep Ghosh

  • Aug 25:

    Webcast link: https://us02web.zoom.us/j/87922267326?pwd=SnE0N0FGMklmVHV3MHp5eVNYL2ZDUT09, Meeting ID: 879 2226 7326, Password: 339970.


    Sparse and compositionally robust inference of microbial ecological networks. ZD Kurtz, CL Müller, ER Miraldi, DR Littman, MJ Blaser, RA Bonneau. PLoS computational biology 11 (5), 2015.
    — Shaikh, Mohd Faraz

    A cell-based model for quorum sensing in heterogeneous bacterial colonies. P Melke, P Sahlin, A Levchenko, H Jönsson. PLoS computational biology 6 (6), e1000819, 2010.
    — Szymon Chrost

    Transition to quorum sensing in an Agrobacterium population: A stochastic model, AB Goryachev, DJ Toh, KB Wee, T Lee, HB Zhang, LH Zhang, PLoS computational biology 1 (4),
    — Md.Ballal Hossen

  • Sept 1:

    Webcast link: https://us02web.zoom.us/j/81542221503?pwd=YXJ0Y0lGNCtMMUZ2MDVZVUpQNzBiZz09, Meeting ID: 815 4222 1503, Password: 650303.


    Schmidt U., Weigert M., Broaddus C., Myers G. (2018) Cell Detection with Star-Convex Polygons. In: Frangi A., Schnabel J., Davatzikos C., Alberola-López C., Fichtinger G. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. MICCAI 2018. Lecture Notes in Computer Science, vol 11071. Springer, Cham.
    — Nastassya Horlova

    D. V. Nicolau Jr., J. F. Hancock, and K. Burrage. Sources of anomalous diffusion on cell membranes: A Monte-Carlo study. Biophys. J., 92:1975–1987, 2007.
    — Jinjing, Xu

    An integrated modelling framework from cells to organism based on a cohort of digital embryos. P Villoutreix, J Delile, B Rizzi, L Duloquin, T Savy, P Bourgine, R Doursat, ... Scientific reports 6, 37438, 2016.
    — Debashis B.

    Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model. A Yakimovich, H Gumpert, CJ Burckhardt, VA Lütschg, A Jurgeit, ... Journal of virology 86 (18), 10123-10137.
    — Vaibhav Sharma