(`A k k @@@ @@@@N kp k EN DB  k     & . 67YG  i     v  I(&  Aho2005A Alber2004  Allen2003@Awasthi1995? Berry2002? Bray2001 Brugal20012 Butler19969 Buttle2001 Calzone2003Campbell1999 Carson20022A Chaturvedi2004 Chen2002 Chen20030=Chicurel2002A Cickovski2004  Ciliberto2003ACoffland20044 Cohen2004 Crampin2004 DeLisi1999@ Doolittle1995?A Forgacs2004Fredberg19969 Gaffney1999 Gillet20030A Glazier2004% Hashimoto2002> Heid2002A Hentschel2004 Hill20040) Hill2004&Holcombe20033Holcombe2003?Holcombe20044)Holcombe20044 Hose2003?) Hose20042 Howell2001 Howell20040A Huang2004 Hunter20044 Hunter2004 Ingber19969A Izaguirre2004( Kromin2004Ladinsky20040 Linne2005 Loew20020'Lorensen19966)Mac Neil20044 Maini1999Manninen20055 Marcelpoil2001 Marsh2001 Marsh2004' Martin19969 Mastronarde2001McIntosh20010@McNally1995??Mitchell1999Mizunuma2001 Mogelsvang2004< Mogilner Morel2001 Muller1996& Neil2003 Neil2003?A Newman20040 Olson2003@Parulkar1995?Pettinen2005% Pickett2002$ Pollack2001 Purves1998  Ramakrishnan2003 Reece1999Saarinen20055 Sankaranarayanan2003 Sanner20030 Schaff20022' Schroeder1996 Shaffer2003Sherratt1999 Sible2003 Slepchenko2002& Smallwood2003 Smallwood2003? Smallwood2004 Smallwood2004) Smallwood2004 Smith2004 Smolander2005> Soll2002& Southgate2003 Southgate2003? Southgate2004) Southgate2004 Stamenovic1996 Sun2002Taattola20055% Takahashi2002  Tambe1996 Taylor2003? Taylor2003? Taylor2003? Taylor2004?A Thomas20040% Tomita20022Tsutsumi2001 Tuft19991 Tyson2003 Vajda1999 Vass20033> Voss2002& Walker20030 Walker2003? Walker20040 Walker2004) Walker2004 Wang19961 Watson20033 Weghorst2003n Wood2003? Wood20040) Wood20042  Wooldridge1996% Yamada20020 Yanai2001 Yli-Harja2005 Yoshida2001% Yugi2002 Zwolak20033ak200332 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak20033002 Zwolak20033 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak20033002 Zwolak200332 Zwolak20033 Zwolak20033 Zwolak20033002 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak20033002 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak200332 Zwolak20033002 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak200332 Zwolak20033002 Zwolak200332 Zwolak200332 Zwolak20033 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak200332 Zwolak20033 Zwolak20033 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak200332 Zwolak20033 Zwolak20033# !  AuthorswJournals Keywords                                k  w Aho, T. Alber, M. Allen, N. A.Awasthi, Vikas Berry, H. Bray, Dennis Brugal, G. Butler, J. P. Buttle, K. F. Calzone, L.Campbell, Neil A. Carson, J. H.Chaturvedi, R.Chen, Authors Hui Chen, K. C. Chicurel, M. Cickovski, T. Ciliberto, A. Coffland, J. Cohen, J.Crampin, E. J. DeLisi, C.Doolittle, Keith W.Ericksson, Geoff Forgacs, G.Fredberg, J. J.Gaffney, E. A.Gillet, AlexandreGlazier, J. A. Hankamer, Ben Hashimoto, K. Heid, P. J. Hentschel, G. Hill, G. Holcombe, M Holcombe, M.Holcombe, W. M. L. Hose, D R Hose, D. R. Howell, K. E. Huang, C. Hunter, P. J. Ingber, D. E.Izaguirre, J. A. Kromin, IgorLadinsky, M. S. Linne, M. L. Loew, L. M.Lorensen, William E. Mac Neil, S. Maini, P. K. Manninen, T.Marcelpoil, R. Marsh, B. J.Martin, Kenneth M.Mastronarde, D. N.McIntosh, J. R.McNally, James G.Mitchell, Lawrence G. Mizunuma, M.Mogelsvang, S.Mogilner, Alex Morel, D. Muller, J. P. Neil, S Mac Newman, S. A. Olson, ArthurParulkar, Guru Pettinen, A.Pickett, C. J. F.Pollack, Gerald H.Purves, William K.Ramakrishnan, N.Reece, Jane B. Saarinen, A.Sankaranarayanan, GaneshSanner, Michel Schaff, J. C.Schroeder, William J.Shaffer, C. A.Sherratt, J. A. Sible, J. C.Slepchenko, B. M. Smallwood, RSmallwood, R. H. Smith, N. P.Smolander, O. P. Soll, D. R. Southgate, J Southgate, J.Stamenovic, D. Sun, HanqiuTaattola, K. L. Takahashi, K. Tambe, M.Taylor, Robert Thomas, G. Tomita, M. Tsutsumi, S. Tuft, S. Tyson, J. J.UQ, Robert Taylor - Vajda, S. Vass, M. T. Voss, E. Walker, D Walker, D. C. Wang, N. Watson, L. T.Weghorst, Suzanne Wood, S. M. Wood, StevenWooldridge, Michael J. Yamada, Y. Yanai, A. Yli-Harja, O. Yoshida, H. Yugi, K. Zwolak, J. W.  tda11th Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (HAPTICS'03)(%Acm Computing Surveys Acm Comput Surv Acta BiotheorPJAnnual Review of Biophysics and Biomolecular Structure Annu Rev Bioph BiomBioinformatics Biophysical Journal Biophys J Biosystems Clin Biomech (Bristol, Avon)41Computing in Science & Engineering Comput Sci Eng$Developmental Biology Dev Biol,)Ieee Intelligent Systems Ieee Intell SystIEEE Trans Nanobioscience J Theor Biol0+Journal of Molecular Histology J Mol Histol not publishednot published yetnot published yet?OmicsProc Natl Acad Sci U S ALHProceedings of the 7th conference on Visualization '96 table of contents`]Proceedings of the ACM symposium on Virtual reality software and technology table of contentsProg Biophys Mol BiolScience Science Traffic  TV *Algorithms*Artificial Intelligence*Cell Physiology*Computer Simulation *Database Management Systems*Models, Biological *Software*Suture Techniques 3-dimensional reconstruction3d reconstruction algorithms alignment alignmentsanchorage-dependent cells Animalsanomalous diffusionArtificial Intelligence83Artificial intelligence Data processing Congresses.automaton model Biology. c. elegans calcium wavesCalcium/*metabolismCalcium/pharmacologycardiac-musclecell Cell Adhesion/drug effects$Cell Communication/*physiology0+Cell Communication/drug effects/*physiology$Cell Culture Techniques/methods$Cell Cycle Proteins/metabolismCell Cycle/physiology$Cell Differentiation/physiologyCell Division/*physiology Cell Line Cell Movement/drug effectsCell Movement/physiologycell physiologyCell physiology.Cell Proliferation$Cell Proliferation/drug effects cell simulation and modelingCell Size/drug effects cell-surfaceCells Motility.Cells, Cultured chemotaxischondrogenesisComparative Study complexes$Computational Biology/*methods@E.6jrv}http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15351133 given to my by Kevin Burrage feb-05'hbDepartment of Computer Science, University of Sheffield, Sheffield, UK. d.c.walker@sheffield.ac.uk6/Yoshida, H. Tsutsumi, S. Mizunuma, M. Yanai, A.e 2001b\A surgical simulation system of skin sutures using a three-dimensional finite element method"Clin Biomech (Bristol, Avon)167< 621-6< Aug11470305Computer Simulation Esthetics Finite Element Analysis Humans Imaging, Three-Dimensional Models, Biological Skin/*surgery *Suture Techniques}OBJECTIVE: To establish a surgical simulation system of skin sutures using a three-dimensional finite element method. DESIGN: Three-dimensional finite element models were developed from point data obtained with a rapid three-dimensional surface-measuring device and postoperative profiles were evaluated using these models. BACKGROUND: Since suturing a wound may result in undesirable skin extrusion, it is important to make the extrusion as inconspicuous as possible. We have investigated a means of determining appropriate suture methods to decrease the extrusion. METHODS: Affected body parts were measured non-invasively with a rapid three-dimensional surface-measuring device. Finite element models were prepared, and an appropriate method for reducing skin extrusion was evaluated by attempting various suturing methods. RESULTS: Two kinds of finite element models were prepared: a conventional spindle model and a modified S-shape model. The height of the extrusion of the modified S-shape model was decreased by 40% in comparison with that of the spindle model. These results agreed with clinical findings. CONCLUSIONS: Due to this surgical simulation system of skin sutures, with a rapid three-dimensional surface-measuring device and three-dimensional finite element analysis, it was possible to design an appropriate suturing method and to evaluate the postoperative skin profiles. The modified S-shape suture method would be a recommendable method. RELEVANCE: Using this surgical simulation system of skin sutures, a surgeon can evaluate an appropriate suturing method before operation. It is expected that this system will reduce a surgeon's labor.~STATUS: p, not read RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: 0268-0033 Journal Article"'.123:?HLTYaelq{lehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11470305'Department of Medical Simulation Engineering, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho Shogoin Sakyo-ku, 606-8507, Kyoto, Japan. yoshida@frontier.kyoto-u.ac.jp @@ &>=?@$A%&'()   <_physiology Humans *Models, Biological Social Behaviorlehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15351133l linguistics Congresses.TM. Wooldridge, J.P. Muller, M. Tambe (eds.) IJCAI '95. ill. ; 24 cm. Second International workshop on Agent Theories, Architectures and j d= Chicurel, M. 2002,&Cell migration research is on the moveScience  295  5555606-609\ JAN 25Science Science1ISI:000173560900011t$Amer Assoc Advancement Science NONEoSTATUS: p, h RATING: **--- TYPE: bio, news article COMMENT: decent small news article; reviews some recent developments/research in cell movement. Q ASKED: N/A ANS GIVEN: - INTEREST: Virtual movement section (1/2 page) 2001 - $8M grant (+ $38M next 5 years) to Cell Migration Consortium (multidisciplinary group at Uni of Virginia) "Cell migration not shared success of sister fields." "Part of the problem is that cell migration has been a fractured disipline, composed of many subfields." "Finally, cell migration starting to emerge as an integrated field" "Round cells extend lamellipodia in random directions, the team found, but square cells send out extensions primarily from their corners" - shape dictates stresses dictates movement. "Based on ... Virtual Cell, the researchers hpe to create a program in which users can test hypotheses about how different parameters - including cell shape, the number and distribution of cellular components, ion and protein concentrations, and reaction rates - influence cell motility." Q RAISED: - CONTRIB: - EXTRA INFO: Times Cited: 8 News Item English Cited References Count: 0 516pd  4;> #-$://000173560900011 Cohen, J. 2004>8Bioinformatics - An introduction for computer scientistsAcm Computing Surveys362122-158 JUN&Acm Comput Surv Acm Comput SurvlISI:000224998400002c Assoc Computing Machineryl.'algorithms languages theory molecular cell biology computer DNA alignments dynamic programming parsing biological sequences hidden-markov-models phylogenetic trees rna and protein structure cell simulation and modeling microarray genomic DNA-sequences alignment simulation databases language rnap0)The article aims to introduce computer scientists to the new field of bioinformatics. This area has arisen from the needs of biologists to utilize and help interpret the vast amounts of data that are constantly being gathered in genomic research-and its more recent counterparts, proteomics and functional genomics. The ultimate goal of bioinformatics is to develop in silico models that will complement in vitro and in vivo biological experiments. The article provides a bird's eye view of the basic concepts in molecular cell biology, outlines the nature of the existing data, and describes the kind of computer algorithms and techniques that are necessary to understand cell behavior. The underlying motivation for many of the bioinformatics approaches is the evolution of organisms and the complexity of working with incomplete and noisy data. The topics covered include: descriptions of the current software especially developed for biologists, computer and mathematical cell models, and areas of computer science that play an important role in bioinformatics.STATUS: np, nr* RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: Times Cited: 0 Article English Cited References Count: 87 869qf#*-./6;DHPU]ahmw$://000224998400002'D=Cohen, J. Brandeis Univ, Dept Comp Sci, Waltham, MA 02454 USA0)Crampin, E. J. Smith, N. P. Hunter, P. J. 2004:3Multi-scale modelling and the IUPS physiome project1$Journal of Molecular Histology357l707-714m SEP\ J Mol Histol J Mol HistolaISI:000225904000007hKluwer Academic Publcross-bridge model muscle-contraction signaling pathway enzyme-reactions systems biology cardiac-muscle cell simulations kinetics myocytepiWe review the development of models of cellular and tissue function and in particular address issues of multi-scale modelling, including the transition from stochastic models to continuum models and the incorporation of cell and tissue structure. The heart is used as an example of linking models at the molecular level to cell, tissue and organ level function.STATUS: p, r ?? RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: Times Cited: 0 Article English Cited References Count: 45 881xy#*-./6;DHPU]ahmw$://000225904000007'Hunter, P. J. Univ Auckland, Bioengn Inst, Private Bag 92019, Auckland 1, New Zealand Univ Auckland, Bioengn Inst, Auckland 1, New Zealand (  Igor Kromin 2004TMDeveloping a prototype visualisation Environment for the visible Cell Project2,Bachelor of Science (Information Technology)  Queensland University of Queenland84"Geoff Ericksson Ben HankamerHonours Visualization& Visualisation and integration of multimodal data sets in Cellular Biology presents a number of challenges. The ability to combine data ranging from atomic to nanometer resolution is not a trivial task, but is extremely beneficial in analyzing the structure and function of a cell. The Visible Cell Project aims to address these needs, however, no concrete requirements criteria or directions have been defined to address these needs. In response to this situation, a prototype system has been developed to address the challenge of defining the requirements and exploring possible future directions in multimodal data visualisation and integration. The prototype was developed as a proof-of-concept guide. Through its development, the high level criteria for visualisation and integration of multimodal data sets have been established. A number of existing visualisation technologies were evaluated and one software package was consequently used for the prototype implementation. While the prototype itself does not present a usable system, it provides the groundwork for future development of functional visualisation and integration systems. The research carried out to realise this project indicates that the future work lies in the areas of data definition, system development and large-scale visualisation.ZqSTATUS: p, h RATING: ***** TYPE: IT honours thesis COMMENT: helpful start Q ASKED: what is visible cell, what visualisation technologies most suitable? ANS GIVEN: AVS/Express was used for prototype, Igor told me VTK might be best for real thing. INTEREST: what software to use Q RAISED: - CONTRIB: good breif, basic intro to cell biology. EXTRA INFO: Not published  4;>KLS!%,XbTNhttp://research.imb.uq.edu.au/~nhamilton/viscell/uploads/IgorKromin_Thesis.pdfRKMarsh, B. J. Mastronarde, D. N. Buttle, K. F. Howell, K. E. McIntosh, J. R. 2001Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography<Proc Natl Acad Sci U S A9852399-406 Feb 2711226251Cell Line Electrons Golgi Apparatus/*ultrastructure Islets of Langerhans/*ultrastructure Models, Biological Organelles/*ultrastructure Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Tomography/*methodsThe positional relationships among all of the visible organelles in a densely packed region of cytoplasm from an insulin secreting, cultured mammalian cell have been analyzed in three dimensions (3-D) at approximately 6 nm resolution. Part of a fast frozen/freeze-substituted HIT-T15 cell that included a large portion of the Golgi ribbon was reconstructed in 3-D by electron tomography. The reconstructed volume (3.1 x 3.2 x 1.2 microm(3)) allowed sites of interaction between organelles, and between microtubules and organellar membranes, to be accurately defined in 3-D and quantitatively analyzed by spatial density analyses. Our data confirm that the Golgi in an interphase mammalian cell is a single, ribbon-like organelle composed of stacks of flattened cisternae punctuated by openings of various sizes [Rambourg, A., Clermont, Y., & Hermo, L. (1979) Am. J. Anat. 154, 455-476]. The data also show that the endoplasmic reticulum (ER) is a single continuous compartment that forms close contacts with mitochondria, multiple trans Golgi cisternae, and compartments of the endo-lysosomal system. This ER traverses the Golgi ribbon from one side to the other via cisternal openings. Microtubules form close, non-random associations with the cis Golgi, the ER, and endo-lysosomal compartments. Despite the dense packing of organelles in this Golgi region, approximately 66% of the reconstructed volume is calculated to represent cytoplasmic matrix. We relate the intimacy of structural associations between organelles in the Golgi region, as quantified by spatial density analyses, to biochemical mechanisms for membrane trafficking and organellar communication in mammalian cells.*BSTATUS: p, h RATING: **--- TYPE: cell bio COMMENT: complex, but valueable, should re-read later. Q ASKED: what we find when we analyse positional relationships between organelles in densely packed region of cytoplasm (from insulin secreting mammalian cell) ANS GIVEN: ER forms close contacts with mitochondria, tans Golgi cisternae... etc. 66% reconstructed volume is calculed to represent cytomplasmic matrix. INTEREST: will use this data in project Q RAISED: how else can data be analysed CONTRIB: better knowledge of cell tomography EXTRA INFO: 0027-8424 Journal Article  +25bcj 'lehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11226251'Boulder Laboratory for 3-D Fine Structure, Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA. % RLTakahashi, K. Yugi, K. Hashimoto, K. Yamada, Y. Pickett, C. J. F. Tomita, M. 2002RLComputational challenges in cell simulation: A software engineering approachIEEE Intelligent Systems175 64-71SEP-OCTIeee Intell SystISI:000178362900013Ieee Computer SocnetworksSTATUS: p, h, should read again RATING: **--- TYPE: comp, SE COMMENT: E-cell could be very important Q ASKED: what simulation systems are out there? what is SE role in cell simulation & what requirements. ANS GIVEN: our E-Cell aims to develop software platforms necessary for whole-cell-scale modeling. INTEREST: says: computer-simulated experiments can help guide wet-lab process, effectively narrowing search space. Q RAISED: - CONTRIB: - EXTRA INFO: Times Cited: 8 Article English Cited References Count: 15 599ym www.e-cell.org '-2>EHfgn2:$://000178362900013'Takahashi, K. Keio Univ, Inst Adv Biosci, 5322 Endo, Fujisawa, Kanagawa 2528520, Japan Keio Univ, Inst Adv Biosci, Fujisawa, Kanagawa 2528520, Japan4.Tambe, M. Muller, J. P. Wooldridge, Michael J. 1996Intelligent agents II : agent theories, architectures, and languages : IJCAI'95 Workshop (ATAL), Montreal, Canada, August 19-20, 1995 : proceedings0)Lecture notes in artificial intelligence. New York Springer 437 p.3540608052 (pbk.)& Phys Sci & Engin QA76 .L4 v.1037{Artificial intelligence Data processing Congresses. Computer architecture Congresses. Computational linguistics Congresses.STATUS: borrowed from Lindsay Wood 18-Mar-05 RATING: **--- TYPE: series of papers. COMMENT: seems very technical - lots of "formal definitions" for aspects of agent models, not very interesting. Q ASKED: - ANS GIVEN: - INTEREST: might have to read if chose agent based modelling. Q RAISED: - CONTRIB: - EXTRA INFO: M. Wooldridge, J.P. Muller, M. Tambe (eds.) IJCAI '95. ill. ; 24 cm. Second International workshop on Agent Theories, Architectures and Languages held in conjunction with the International Joint Conference on Artificial Intelligence. International Workshop on Agent Theories, Architectures, and Languages (2nd : 1995 : Montreal, Quebec). International Joint Conference on Artificial Intelligence (14th : 1995 : Montreal, Quebec),-4:?T[^$(/4>  Robert Taylor 2003?F?#h# Multimodal Interaction - Historical & Cognitive Perspectiver not publishedThis paper is the first of a three part series that will look at the area of multimodal interaction particularly in relation to information technology systems. It will look at the definitions, history, physiology and psychology of multimodal interaction and other closely related concepts. It will discuss various conceptual uses for and advantages/disadvantages of, multimodal interaction as well as making comparisons to unimodal interaction, and introducing the concept of multimodality as a means of human computer interaction.n !STATUS: p, h RATING: *---- TYPE: haptics COMMENT: some good definitions, early "put that there" room, otherwise useless. Q ASKED: look at definitions, history, and psycology of multimodal interaction ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: part 1 of 3 part series.o  *14z{81not known - given to me by Ralf Muhlberger feb-05  Robert Taylor 2003?82#h# Multimodal Interaction - Enabling Technologies"This paper is the second of a three paper series that examines computer based multimodal interaction. In this paper various technologies used to facilitate multimodal interaction are categorised and examined. Also discussion is given relating the various limitations and potentials of theses devices and systems, to the hypothesis that multimodal interaction is underutilised, under-researched, and under-developed in relation to humancomputer interaction, particularly when compared to development in other areas of information technology.STATUS: p, h RATING: *---- TYPE: haptics COMMENT: basic intro Q ASKED: categorises and examines various technologies & discusses limitations ANS GIVEN: specialized hardware 3 groups: physical interaction devices (data gloves, mice), sensor systems (microphones, position tracking, gesture recognition) & output devices (speakers, heads-up displays, CRT etc). INTEREST: interesting "super cilla skin prototype" haptic device & gloves Q RAISED: - CONTRIB: - EXTRA INFO: part 2 of 3 part series  *14?@Gjr81not known - given to me by Ralf Muhlberger feb-05  j81Smallwood, R. H. Holcombe, W. M. L. Walker, D. C.5 2004PJDevelopment and validation of computational models of cellular interaction$Journal of Molecular Histology357659-665;SEP 2004 J Mol Histol J Mol HistolISI:000225904000002Kluwer Academic Publcontact-inhibited cells anchorage-dependent cells erythrocyte cytoskeleton differential adhesion computer-simulations theoretical-models large-deformation automaton model proliferation tensegrityg4In this paper we take the view that computational models of biological systems should satisfy two conditions they should be able to predict function at a systems biology level, and robust techniques of validation against biological models must be available. A modelling paradigm for developing a predictive computational model of cellular interaction is described, and methods of providing robust validation against biological models are explored, followed by a consideration of software issues.$lZqSTATUS: p, h RATING: ***** TYPE: comp, cell biology. COMMENT: very good & very relevant Q ASKED: modelling paradigm for predictive model of cellular interaction. ANS GIVEN: should predict at biology level (build on known properties of cells) & robust techniques to validate against biological models. INTEREST: good references of work in simulating epitelial tissue. good references. Q RAISED: what would happen if sub-optimal percentage of stem cells. what are wound healing advantages to enriching skin stem cell population. CONTRIB: not huge EXTRA INFO: Times Cited: 0 Article English Cited References Count: 29 881xy  6=@YZa08&0$://000225904000002'Smallwood, R. H. Univ Sheffield, Dept Comp Sci, 211 Portobello St, Sheffield S1 4DP, S Yorkshire, England Univ Sheffield, Dept Comp Sci, Sheffield S1 4DP, S Yorkshire, EnglandJCStamenovic, D. Fredberg, J. J. Wang, N. Butler, J. P. Ingber, D. E.i 1996PI*A microstructural approach to cytoskeletal mechanics based on tensegrity= J Theor Biol 181<2= 125-36 Jul 218935591Animals Cytoskeleton/*ultrastructure Engineering Mathematics Models, Biological Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Stress, MechanicalMechanical properties of living cells are commonly described in terms of the laws of continuum mechanics. The purpose of this report is to consider the implications of an alternative approach that emphasizes the discrete nature of stress bearing elements in the cell and is based on the known structural properties of the cytoskeleton. We have noted previously that tensegrity architecture seems to capture essential qualitative features of cytoskeletal shape distortion in adherent cells (Ingber, 1993a; Wang et al., 1993). Here we extend those qualitative notions into a formal microstructural analysis. On the basis of that analysis we attempt to identify unifying principles that might underlie the shape stability of the cytoskeleton. For simplicity, we focus on a tensegrity structure containing six rigid struts interconnected by 24 linearly elastic cables. Cables carry initial tension ("prestress") counterbalanced by compression of struts. Two cases of interconnectedness between cables and struts are considered: one where they are connected by pin-joints, and the other where the cables run through frictionless loops at the junctions. At the molecular level, the pinned structure may represent the case in which different cytoskeletal filaments are cross-linked whereas the looped structure represents the case where they are free to slip past one another. The system is then subjected to uniaxial stretching. Using the principal of virtual work, stretching force vs. extension and structural stiffness vs. stretching force relationships are calculated for different prestresses. The stiffness is found to increase with increasing prestress and, at a given prestress, to increase approximately linearly with increasing stretching force. This behavior is consistent with observations in living endothelial cells exposed to shear stresses (Wang & Ingber, 1994). At a given prestress, the pinned structure is found to be stiffer than the looped one, a result consistent with data on mechanical behavior of isolated, cross-linked and uncross-linked actin networks (Wachsstock et al., 1993). On the basis of our analysis we concluded that architecture and the prestress of the cytoskeleton might be key features that underlie a cell's ability to regulate its shape.xSTATUS: p, nr RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: 0022-5193 Journal Article !(+,-49BFNS[_fkujdhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8935591'd]Department of Biomedical Engineering, Boston University, MA 02215, USA. dimitrije@enga.bu.edudP& @9Slepchenko, B. M. Schaff, J. C. Carson, J. H. Loew, L. M.  2002NHComputational cell biology: Spatiotemporal simulation of cellular events<6Annual Review of Biophysics and Biomolecular Structure31423-441.'Annu Rev Bioph Biom Annu Rev Bioph BiomISI:000176545500017Annual Reviewsmodel simulation kinetics diffusion cell physiology rna trafficking stochastic simulation calcium waves virtual cell sensitivity environment recordings framework diffusion pathwaysThe field of computational cell biology has emerged within the past 5 years because of the need to apply disciplined computational approaches to build and test complex hypotheses on the interacting structural, physical, and chemical features that underlie intracellular processes. To meet this need, newly developed software tools allow cell biologists and biophysicists to build models and generate simulations from them. The construction of general-purpose computational approaches is especially challenging if the spatial complexity of cellular systems is to be explicitly treated. This review surveys some of the existing efforts in this field with special emphasis on a system being developed in the authors' laboratory, Virtual Cell. The theories behind both stochastic and deterministic simulations are discussed. Examples of respective applications to cell biological problems in RNA trafficking and neuronal calcium dynamics are provided to illustrate these ideas.04$STATUS: p, h RATING: **--- TYPE: cell bio COMMENT: okay, contains lots of terms I should learn, but talks about intra-cellular stuff, & most algorithms reviewed seem to be maths; not proper 3d stuff. Q ASKED: survey/reviews existing efforts ito construct general-purpose computational approaches (harder still if spatial complexity of cullar systems not explicidly treated) - special emphasis on Virtual Cell (in author's lab). ANS GIVEN: describes StochSim, MCell & Virtual Cell INTEREST: Terms I should learn: ordinary differential equation (ODE), partial differential equation (PDE), finite volume method, piecewhise linear interpolation function, brownian random wlks, monte carlo (again), gillespie algorithm, cable theory. Should check out software... some interesting ideas in software discussion: > Stochsim - "multi-state molecules" encoded with series binary flags, > MCELL - user input though special model description language (MDL) files. MDL files are parsed, and corresponding C++ objects created & executed according to user instruction. > Uses 3D spatial partitioning ? > Virtual Cell - interesting architecture... Q RAISED: dynamic shape changes in reaction volume will have interesting stochastic effects. CONTRIB: - EXTRA INFO: Times Cited: 17 Review English Cited References Count: 49 568mg  +25(px$://000176545500017'Slepchenko, B. M. Univ Connecticut, Ctr Hlth, Ctr Biomed Imaging Technol, W Hartford, CT 06117 USA Univ Connecticut, Ctr Hlth, Ctr Biomed Imaging Technol, W Hartford, CT 06117 USA<6R Smallwood M Holcombe D Walker J Southgate S Mac Neil 2003>8Computational modelling of the social behaviour of cellsnot published yet?STATUS: p, h RATING: ***-- TYPE: comp, modelling, math COMMENT: not bad Q ASKED: review cellular interaction models & propose new modelling paradigm to combine rule-based agents & physical model. ANS GIVEN: interesting hierarchial/multiscale model put forward... physical forces determines cell morphology, determines intra-cellular relationships, affects agents rules (death, division, differentiation) affects physical forces. INTEREST: explains epithelial cell cycle, has review. Q RAISED: - CONTRIB: - EXTRA INFO: Not published  8?BIJQ .(not known - given to me by Kevin BurrageRKR Smallwood M Holcombe D Walker D R Hose Steven Wood S Mac Neil J Southgate\ 2003?p@:Modelling emergent order: from individual cells to tissuesnot published yetD? `wSTATUS: np, nr RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO:T"),-.5:CGOT\`glv0*not found - Kevin B gave to me as word doc xWalker, D. C. Hill, G. Wood, S. M. Smallwood, R. H. Southgate, J.R 2004PI*Agent-based computational modeling of wounded epithelial cell monolayersr IEEE Trans Nanobiosciencel3}3l 153-63 Sepu15473067PJAlgorithms Artificial Intelligence Calcium/pharmacology Cell Adhesion/drug effects Cell Communication/drug effects/*physiology Cell Cultur:4Gaffney, E. A. Maini, P. K. Sherratt, J. A. Tuft, S. 1999VOThe mathematical modelling of cell kinetics in corneal epithelial wound healing1 J Theor Biol 19711f 15-40 Mar 710047473Animals Cell Differentiation/physiology *Computer Simulation Epithelium, Corneal/*injuries/pathology Mitosis/physiology *Models, Biological Rats Wound Healing/*physiology*#This paper considers the comparison of experimental spatial and temporal data of mitotic rates measured during corneal epithelial wound healing (CEWH) of a rat model with the predictions of a computer modelling framework. We begin by briefly showing that previous models, used in the study of corneal epithelial wound healing speeds, are inadequate for the study of cell kinetics. We proceed to formulate a new modelling framework more suited to such a study. This framework is simulated in its simplest form, and the results from this motivate a new realisation of the modelling framework, including a caricature of age structuring. Finally, a model with a simple representation of juxtacrine signalling is considered. The final model captures many, though not all, of the trends of the experimental data. This paper thus lays a foundation for the modelling of the cell kinetics of corneal epithelial wound healing, and yields valuable insight regarding the important mechanisms a model should consider in order to reproduce the observed experimental trends.STATUS: p, h some. RATING: ***-- TYPE: math, bio COMMENT: quite interesting, probably not relevant though Q ASKED: can we create better model of conrneal (front of eye) wound healing (CEWH), to match real results ANS GIVEN: yes, use heterogenic modelling framework with proliferating & quiescent cells, also emphasise important of coupling spatial heterogenity and age structure. INTEREST: - Q RAISED: - CONTRIB: better CEWH model & understanding EXTRA INFO: 0022-5193 Journal Article %29<klslehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10047473'ztCentre for Mathematical Biology, Mathematical Institute, 24-29 St. Giles, Oxford OX1 3LB, UK. gaffney@maths.ox.ac.ukA Izaguirre, J. A. Chaturvedi, R. Huang, C. Cickovski, T. Coffland, J. Thomas, G. Forgacs, G. Alber, M. Hentschel, G. Newman, S. A. Glazier, J. A. 2004JC*CompuCell, a multi-model framework for simulation of morphogenesisBioinformatics207  1129-1137 MAY 1BioinformaticsISI:000221139700016Oxford Univ Pressheparin-binding domain pattern-formation vertebrate limb mesenchymal condensation embryonic limb cell-surface model chondrogenesis fibronectin mechanismsMotivation: CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. Results: We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud.STATUS: p, nr RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: Times Cited: 6 Article English Cited References Count: 35 816wj !(+,-49BFNS[_fku$://000221139700016/'F?Izaguirre, J. A. Univ Notre Dame, Dept Comp Sci & Engn, Notre Dame, IN 46556 USA Univ Notre Dame, Dept Comp Sci & Engn, Notre Dame, IN 46556 USA Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA Univ Missouri, Dept Phys & Biol, Columbia, MO 65211 USA Univ Notre Dame, Dept Math, Notre Dame, IN 46556 USA Emory Univ, Dept Phys, Atlanta, GA 30332 USA New York Med Coll, Dept Cell Biol & Anat, Valhalla, NY 10595 USA Indiana Univ, Dept Phys, Bloomington, IN 47405 USA Indiana Univ, Dept Biol, Bloomington, IN 47405 USA Indiana Univ, Biocomplex Inst, Bloomington, IN 47405 USAo on the constructive volume methodology, we have developed sculpting tools as volumes, with each properties and size, distribution for elements, and rules of the interaction between the volumetric data and the tools. The sculpting tools are controlled directly by the 6-DOF haptic input to simulate realistic sculpting operations, in applying the computed model and tool dynamics while interacting with the volume. Both synthetic volumetric data and medical scan volumes are experimented using the 6-DOF PHANToM Desktop haptic interface.STATUS: p, half-h RATING: *---- TYPE: haptics COMMENT: tiny bit info, pretty useless Q ASKED: propose virtual haptic sulpting system ANS GIVEN: sculpting mechanisms, peeling, melting etc. INTEREST: not much, breif talk of volume visualization - marching cubes & 2 main haptic rendering techniques (direct volume redering - voxels & surface haptic rendering - polygons) Q RAISED: - CONTRIB: - EXTRA INFO:$/69VW^u}f_http://portal.acm.org/citation.cfm?id=585755&dl=GUIDE&coll=GUIDE&CFID=41210719&CFTOKEN=8637770803@AHAHMWlehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15142761'\VBioengineering Institute, University of Auckland, New Zealand. p.hunter@auckland.ac.nz' $ Pollack, Gerald H. 2001VOCells, gels and the engines of life : a new, unifying approach to cell function  Seattle, WAC  Ebner & Sons xiv, 305 p.b*$0962689513 (cased) 0962689521 (pbk.)VPBiol Sciences QH631 .P65 2001 DUE 29-03-05 +1 HOLD Biol Sciences QH631 .P65 2001Cell physiology.STATUS: borrowed from bio sci lib in mar-05, in high-demand. read whole thing. RATING: ***** TYPE: - COMMENT: very interesting ideas/paradigms, written in simple English. Q ASKED: - ANS GIVEN: - INTEREST: > When you break/split/pierce cell it usually keeps living - even though membrane bady broken and insides exposed > Many mammilian cells (skin=3-6%, cardiac muscle=20%) under constant wounded state. > Lipid membrane has abundant proteins causing "leakiness" - same as holes in membrane leaky. > Is not clear how channel that passes one solute primarily, systematically excludes others of the set; particually smaller members (the dog-door problem). > Pumps & channel analogy might be flawed. > Cells so crowded, most cell water forms about 5-6 layers (molecules deep); maximum of 10 layers. > Cell water is mostly structured in layers (aligning with surrounding proteins) - unlike bulk water - thus has different properties - more gel like? > Cell water excludes ions - moreso sodium than potassium - explains why sodium concentration lower inside cell, but potassium concentraion much higher inside cell. > Phase transition hugely important in cell. Divalent cations condense strands & expel water. > Vescicle expand greatly as they exit membrane - proteins in vescicle unravel. > Volume microtubular network just under 20% Q RAISED: - CONTRIB: - EXTRA INFO: Brad Marsh recommended this book mid-march in e-mail. Gerald H. Pollack. ill. (some col.) ; 25 cm.NOV\afmp8@DKPZ\Purves, William K. 1998$Life : the science of biology ,&Sunderland, Mass. Salt Lake City, Utah @:Sinauer Associates ; [Distributed by] W.H. Freeman and Co.1243 p. 5th(!0716733250 0716728699 (hardcover)2,Biol Sciences QH308.2 .P87 1998 DUE 05-04-05Biology.ZqSTATUS: borrowed from Jim Feb-05 RATING: ***** TYPE: bio COMMENT: great book, good general intro to cell biology Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: William K. Purves ... [et al.] ill. (some col.), col. maps ; 29 cm. Rev. ed. of: Life, the science of biology / William K. Purves, Gordon H. Orians, H. Craig Heller. 4th ed. c1995.l !(.3:ADrszZTGanesh Sankaranarayanan Suzanne Weghorst Michel Sanner Alexandre Gillet Arthur Olson 2003>8Role of Haptics in Teaching Structural Molecular Biologyha11th Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (HAPTICS'03) 363 0-7695-1890-7<6Physical models such as ball-and-stick have long been used in teaching basic chemistry and structural molecular biology. As the size and complexity of known molecular structures increases, it is difficult if not impossible to show all of their features in a physical model alone. Recent advances in automated model fabrication technology now afford physical models of more complex molecular structures. In this multi-institutional collaborative project we are creating multi-modality enhancements of such tangible models by superimposing graphical (augmented reality) information on top of the fabricated physical models, by incorporating support for voice commands, and by providing haptic feedback.The user of such an interface can request a variety of overlay representations and can interact with these virtual enhancements haptically while manipulating the physical model. This multi-modality interface appears to be quite intuitive for observing complex molecular structure. We are currently evaluating its usefulness in teaching molecular biology to high school students.rSTATUS: p, h RATING: *---- TYPE: haptics COMMENT: - Q ASKED: we are enhancing physical models with voice commands and haptic feedback. how effective is it? ANS GIVEN: claims quite effective & are currently evaluating usefulness in teaching molecular biology to high school students. INTEREST: use PHANTOM device & python, can display force vector field. Q RAISED: - CONTRIB: - EXTRA INFO:  *1456=&fnry~http://csdl.computer.org/comp/proceedings/haptics/2003/1890/00/18900363abs.htm http://portal.acm.org/citation.cfm?id=797552&dl=GUIDE&coll=GUIDE&CFID=41210719&CFTOKEN=86377708@:William J. Schroeder Kenneth M. Martin William E. Lorensen 1996d]The Design and Implementation Of An Object-Oriented Toolkit For 3D Graphics And Visualization NHProceedings of the 7th conference on Visualization '96 table of contents 93-ffISBN:0-89791-864-9vpThe Visualization Toolkit (vtk) is a freely available C++ class library for 3D graphics and visualization. In this paper we describe core characteristics of the toolkit. This includes a description of object-oriented models for graphics and visualization; methods for synchronizing system execution; a summary of data representation schemes; the role of C++; issues in portability across PC and Unix systems; and how we automatically wrap the C++ class library with interpreted languages such as Java and Tcl. We also demonstrate the capabilities of the system for scalar, vector, tensor, and other visualization techniques.STATUS: p, h RATING: ***-- TYPE: comp, programming, vtk specific COMMENT: not bad Q ASKED: what are core characteristics of VTK ANS GIVEN: describes implementation, gives couple examples INTEREST: might use vtk - is platform independent & free, but just higher level version of OpenGL including some datatypes like polygons...? Q RAISED: - CONTRIB: - EXTRA INFO: Igor Kromin said real VisibleCell application should be written using vtk.  BILST[LTX_dn^Xhttp://public.kitware.com/VTK/pdf/dioot.pdf http://portal.acm.org/citation.cfm?id=245018  Z<f Alex Mogilner$#s# Homepage of Alex Mogilners University of CaliforniaSTATUS: visited couple of time RATING: - TYPE: - COMMENT: seems to be useful info - should contact maybe Q ASKED: - ANS GIVEN: - INTEREST: Cell motility and cell division. Has review & links to relevant papers Q RAISED: - CONTRIB: - EXTRA INFO:&(-29<jkrw,&http://www.math.ucdavis.edu/~mogilner/*#Morel, D. Marcelpoil, R. Brugal, G.c 2001f_A proliferation control network model: the simulation of two-dimensional epithelial homeostasist Acta BiotheorE494a 219-3411804235Cell Cycle/physiology Cell Differentiation/physiology Cell Division/*physiology Cell Movement/physiology *Computer Simulation Epithelial Cells/*cytology Feedback, Biochemical/physiology Homeostasis/*physiology Humans Signal Transduction/physiology Despite the recent progress in the description of the molecular mechanisms of proliferation and differentiation controls in vitro, the regulation of the homeostasis of normal stratified epithelia remains unclear in vivo. Computer simulation represents a powerful tool to investigate the complex field of cell proliferation regulation networks. It provides huge computation capabilities to test, in a dynamic in silico context, hypotheses about the many pathways and feedback loops involved in cell growth and proliferation controls. Our approach combines a model of cell proliferation and a spatial representation of cells in 2D using the Voronoi graph. The cell proliferation model includes intracellular (cyclins, Cyclin Dependent Kinases - CDKs. Retinoblastoma protein - Rb, CDK inhibitors) and extracellular controls (growth and differentiation factors, integrins). The Voronoi graph associates a polygon with every cell and the set of these polygons defines the tissue architecture. Thus, the model provides a quantitative model of extracellular signals and cell motility as a function of the neighborhood during time dependent simulations. The 2D simulations illustrate the influence of the microenvironment on cell proliferation in basal layers of stratified epithelia and of differential adherence in keratinocytes differentiation and related upward migration. Our results particularly show the role of CDK inhibitors (mainly the protein p27) in the Rb dependent control pathway of the transition from the G1 to S phase of the cell cycle.H`STATUS: p, h RATING: ***-- TYPE: comp, bio COMMENT: nice idea (Voroni graph to represent cells), limited success, bit abstract? Q ASKED: can we combine cell proliferation model with spatial 2D Voronoi graph to good effect? ANS GIVEN: limited success, model hard to handle because it's large number of parameters. INTEREST: different cells represented: stem cells, transit amplifing and committed cells which migrat upwards. Uses mirror effect at boundary. Once better for 2D, interesting to improve using 3D Voroni graph. Q RAISED: can we do this better. CONTRIB: - EXTRA INFO: 0001-5342 Journal Article  ,36<D/6;Elehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11804235'Equipe de Reconnaissance des Formes et Microscopie Quantitative, Laboratoire TIMC-IMAG, UMR CNRS 5525, Institut Albert Bonniot, Faculte de Medecine, La Tronche, France. dmorel@imag.frpjPettinen, A. Aho, T. Smolander, O. P. Manninen, T. Saarinen, A. Taattola, K. L. Yli-Harja, O. Linne, M. L. 2005XRSimulation tools for biochemical networks: evaluation of performance and usabilityBioinformatics213} 357-63 Feb 1n15358616tnMOTIVATION: Simulation of dynamic biochemical systems is receiving considerable attention due to increasing availability of experimental data of complex cellular functions. Numerous simulation tools have been developed for numerical simulation of the behavior of a system described in mathematical form. However, there exist only a few evaluation studies of these tools. Knowledge of the properties and capabilities of the simulation tools would help bioscientists in building models based on experimental data. RESULTS: We examine selected simulation tools that are intended for the simulation of biochemical systems. We choose four of them for more detailed study and perform time series simulations using a specific pathway describing the concentration of the active form of protein kinase C. We conclude that the simulation results are convergent between the chosen simulation tools. However, the tools differ in their usability, support for data transfer to other programs and support for automatic parameter estimation. From the experimentalists' point of view, all these are properties that need to be emphasized in the future.~STATUS: p, not read RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: 1367-4803 Journal Article"'.123:?HLTYaelq{lehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15358616'}Institute of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland. antti.pettinen@tut.fi @9Mogelsvang, S. Marsh, B. J. Ladinsky, M. S. Howell, K. E. 2004^WPredicting function from structure: 3D structure studies of the mammalian Golgi complex7Traffic55, 338-45 May<15086783Animals Golgi Apparatus/chemistry/*metabolism/*ultrastructure Mammals Microscopy, Electron, Scanning Models, Molecular Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Tomography, X-Ray Computed3D electron tomography studies of the structure of the mammalian Golgi complex have led to four functional predictions (1). The sorting and exit site from the Golgi comprises two or three distinct trans-cisternae (2). The docking of vesicular-tubular clusters at the cis-face and the fragmentation of trans-cisternae are coordinated (3). The mechanisms of transport through, and exit from, the Golgi vary with physiological state, and in different cells and tissues (4). Specialized trans-ER functions in the delivery of ceramide to sphingomyelin synthase in the trans-Golgi membrane, for the regulated sorting via sphingolipid-cholesterol-rich domains. These structure-based predictions can now be tested using a variety of powerful cell and molecular tools.BmSTATUS: p, h RATING: ***-- TYPE: cell bio COMMENT: complex, but valueable, should re-read later. Q ASKED: can now tests functional predictions using 3D electron tomography studies using variety of "powerful cell and molecular tools" ANS GIVEN: observational stuff INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: 1398-9219 Journal Article Review Review, Tutorial  +25cj  $+0:lehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15086783'University of Colorado School of Medicine, Department of Cell and Developmental Biology, University of Colorado Health Sciences Center, Denver, CO 80262, USA.@ D ~Allen, N. A. Calzone, L. Chen, K. C. Ciliberto, A. Ramakrishnan, N. Shaffer, C. A. Sible, J. C. Tyson, J. J. Vass, M. T. Watson, L. T. Zwolak, J. W. 20034.*Modeling regulatory networks at Virginia Tech Omics{7M3t 285-99 Fall14583117Animals Cell Cycle/physiology Cell Cycle Proteins/metabolism *Cell Physiology Computational Biology/*methods Computer Simulation Gene Expression Regulation Gene Expression Regulation, Developmental *Models, Biological Ovum/cytology/metabolism Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. *Software Virginia Yeasts/cytology/growth & development/metabolism\VThe life of a cell is governed by the physicochemical properties of a complex network of interacting macromolecules (primarily genes and proteins). Hence, a full scientific understanding of and rational engineering approach to cell physiology require accurate mathematical models of the spatial and temporal dynamics of these macromolecular assemblies, especially the networks involved in integrating signals and regulating cellular responses. The Virginia Tech Consortium is involved in three specific goals of DARPA's computational biology program (Bio-COMP): to create effective software tools for modeling gene-protein-metabolite networks, to employ these tools in creating a new generation of realistic models, and to test and refine these models by well-conceived experimental studies. The special emphasis of this group is to understand the mechanisms of cell cycle control in eukaryotes (yeast cells and frog eggs). The software tools developed at Virginia Tech are designed to meet general requirements of modeling regulatory networks and are collected in a problem-solving environment called JigCell.xSTATUS: p, nr RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: 1536-2310 Journal Article !(+,-49BFNS[_fkulehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14583117a'zsThe Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA./F?Vikas Awasthi Keith W. Doolittle Guru Parulkar James G. McNally. 1995?KLECell Tracking using a Distributed Algorithm for 3D Image Segmentation Washington UniversityT 200522/4/05TMWe have developed and tested an automated method for simultaneous 3D tracking of numerous, fluorescently-tagged cells. The procedure uses multiple thresholding to segment individual cells at a starting timepoint, and then iteratively applies a template-matching algorithm to locate a particular cell's position at subsequent timepoints. To speed up the method, we have developed a distributed implementation in which template matching is carried out in parallel on several different server machines. The distributed implementation showed a monotonic decrease in response time with increasing number of servers (up to 15 tested), demonstrating that the tracking algorithm is well suited to parallelization, and that nearly real-time performance could be expected on a parallel processor. Of four different template matching statistics tested for 3D tracking of amebae from the cellular slime mold Dictyostelium discoideum, we found that the automated procedure performed best when using a correlation statistic for matching. Using this statistic, the method achieved a 98.5% success rate in correctly identifying a cell from one timepoint to the next. This method is now being used regularly for 3D tracking of normal and mutant cells of D. discoideum, and as such provides a means to quantify the motion of many cells within a three-dimensional tissue mass.STATUS: online article, old & not publised, p, h RATING: **--- TYPE: comp COMMENT: relevant, but not published means bad Q ASKED: how can we track in vitro cell movement in 3d ANS GIVEN: nearest neighbor often works, but use template matching (based on object's size, shape & intensity) when NN fails. INTEREST: Talks about method to manually track cells (use cross section & pick center voxel), and compare this to automated tracking results. Defined miss as: when manual & automatic cell positions deviate by more than half cell radius. 2 minute intervals - collected 256x256x64x60 (x,y,z,t) at 2 bytes per pixel = 500MB of data. (Individual D discoideum cells labeled with fluorescent dye.) Two step process: (1) at first timestep, cells identified by maximum thresholding. For each thresholded cell, a template is extracted around that cell's center of mass. (2) template used to find position of best match at the next timestep - which determines a new template, and template matching applied to the next time point. Some equations for difference, normalized cross correlation & correlation coefficient too. Also disscussed distributed implementation (single client with data, multiple servers). Q RAISED: - CONTRIB: - EXTRA INFO: Old and not published. :(018>CKRUz{19@9http://rex.nci.nih.gov/RESEARCH/basic/lrbge/tracking.html ^F  Robert Taylor 2003?@9#h# Multimodal Interaction - Applications and Development\ not publisheddThis, the final work of a three paper series, examines computer based multimodal interaction by providing a review of literature relating to current existing multimodal systems and prototypes. The underlying suggestion of this series is that multimodal interaction is historically and currently underutilised, under-researched, and under-developed in relation to human-computer interaction. The literature reviewed in this paper is examined in relation to this hypothesis and further discussion relating to why this may be so, is given.STATUS: p, h RATING: *---- TYPE: haptics COMMENT: interesting applications, but that's about all Q ASKED: what multimodal systems are out there, what are trends & design issues. ANS GIVEN: all intuitive stuff INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: part 3 of 3 part series.G *14bcj81not known - given to me by Ralf Muhlberger feb-05  Robert Taylor 2004?u81#h# An investigation of mixed reality interaction not publishedThis paper describes an investigation of interactional issues relating to mixed reality (M.R.) systems, with a particular focus on physical interaction devices. It is roughly divided into three sections; The first section provides a background and current view of developments in augmented reality and virtual reality and explores various applications of these systems including their uses in such areas as telerobotics and wearable computing. The next section outlines a hypothesis that roughly states that limitations of the physical interaction devices of M.R. systems, can affect (possibly detrimentally) the way users interact with those systems, and includes the results of some field research conducted into this phenomenon. The final section gives discussion and analysis of this field work. It identifies usability and design issues arising from this fieldwork and explores principles for the design of better M.R. physical interaction devices, based on various published research.STATUS: p, h RATING: *---- TYPE: haptics COMMENT: some interesting technologies (eg: dragonfly, playing cards), some simple qualiative stuff Q ASKED: what are limitations of haptic devices ANS GIVEN: fluffy. 4 students used QUT haptic feedback bench, grip controller not used overly well - eg: can only comfortably rotate outstretched hand 220 degrees, students did not think to use both hand to rotate further & gave up. INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO:  *140)not known - given to me by Ralf MulbergerHAWalker, D. C. Hill, G. Wood, S. M. Smallwood, R. H. Southgate, J.= 2004PI*Agent-based computational modeling of wounded epithelial cell monolayersE IEEE Trans Nanobioscience33 153-63 Sep15473067PJAlgorithms Artificial Intelligence Calcium/pharmacology Cell Adhesion/drug effects Cell Communication/drug effects/*physiology Cell Culture Techniques/methods Cell Line Cell Movement/drug effects Cell Proliferation/drug effects Cell Size/drug effects Cells, Cultured Comparative Study Computer Simulation Dose-Response Relationship, Drug Epithelial Cells/drug effects/*pathology/*physiology Humans *Models, Biological Research Support, Non-U.S. Gov't Urothelium/cytology/drug effects/physiopathology Wound Healing/drug effects/*physiology Wounds, Penetrating/*pathology/*physiopathologyb\Computational modeling of biological systems, or in silico biology, is an emerging tool for understanding structure and order in biological tissues. Computational models of the behavior of epithelial cells in monolayer cell culture have been developed and used to predict the healing characteristics of scratch wounds made to urothelial cell cultures maintained in low- and physiological [Ca2+] environments. Both computational models and in vitro experiments demonstrated that in low exogenous [Ca2+], the closure of 500-microm scratch wounds was achieved primarily by cell migration into the denuded area. The wound healing rate in low (0.09 mM) [Ca2+] was approximately twice as rapid as in physiological (2 mM) [Ca2+]. Computational modeling predicted that in cell cultures that are actively proliferating, no increase in the fraction of cells in the S-phase would be expected, and this conclusion was supported experimentally in vitro by bromodeoxyuridine incorporation assay. We have demonstrated that a simple rule-based model of cell behavior, incorporating rules relating to contact inhibition of proliferation and migration, is sufficient to qualitatively predict the calcium-dependent pattern of wound closure observed in vitro. Differences between the in vitro and in silico models suggest a role for wound-induced signaling events in urothelial cell cultures. STATUS: p, nr* RATING: - TYPE: - COMMENT: - Q ASKED: - ANS GIVEN: - INTEREST: - Q RAISED: - CONTRIB: - EXTRA INFO: 1536-1241 Evaluation Studies Journal Article Validation Studies http://www.dcs.shef.ac.uk/~dawn/research/research.html << more papers - Dawn Walkerr"),-.5:CGOT\`glvlehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15473067'TNDepartment of Computer Science, University of Sheffield, Sheffield S1 4DP, UK.A Z$://0002211397000160ISI:000221139700016e*Bioinformatics^BCompuCell, a multi-model framework for simulation of morphogenesis& 1129-1137fIzaguirre, J. A. Chaturvedi, R. Huang, C. Cickovski, T. Coffland, J. Thomas, G. Forgacs, G. Alber, M. Hentschel, G. Newman, S. A. Glazier, J. A.heparin-binding domain pattern-formation vertebrate limb mesenchymal condensation embryonic limb cell-surface model chondrogenesis fibronectin mechanisms'\?Izaguirre, J. A. Univ Notre Dame, Dept Comp Sci & Engn, Notre Dame, IN 46556 USA Univ Notre Dame, Dept Comp Sci & Engn, Notre Dame, IN 46556 USA Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA Univ Missouri, Dept Phys & Biol, Columbia, MO 65211 USA Univ Notre Dame, Dept Math, Notre Dame, IN 46556 USA Emory Univ, Dept Phys, Atlanta, GA 30332 USA New York Med Coll, Dept Cell Biol & Anat, Valhalla, NY 10595 USA Indiana Univ, Dept Phys, Bloomington, IN 47405 USA Indiana Univ, Dept Biol, Bloomington, IN 47405 USA Indiana Univ, Biocomplex Inst, Bloomington, IN 47405 USAhMotivation: CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. Results: We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud.\?Times Cited: 6 Article English Cited References Count: 35 816wj:Bioinformatics Bioinformatics.Oxford Univ Press720 MAY 1 2004Desktop haptic interface.STATUS: p, half-h RATING: *---- TYPE: haptics COMMENT: tiny bit info, pretty useless Q ASKED: propose virtual haptic sulpting system ANS GIVEN: sculpting mechanisms, peeling, melting etc. INTEREST: not much, breif talk of volume visualization - marching cubes & 2 main haptic rendering techniques (direct volume redering - voxels & surface haptic rendering - polygons) Q RAISED: - CONTRIB: - EXTRA INFO:$/69VW^u}f_http://portal.acm.org/citation.cfm?id=585755&dl=GUIDE&coll=GUIDE&CFID=41210719&CFTOKEN=86377708  p\(%fluorescence correlation spectroscopy framework Gene Expression Regulation,)Gene Expression Regulation, Developmental genomegenomic DNA-sequences$Golgi Apparatus/*ultrastructure85Golgi Apparatus/chemistry/*metabolism/*ultrastructureheparin-binding domainhidden-markov-modelsHomeostasis/*physiology Humans Imaging, Three-Dimensional$!Information Storage and RetrievalInternational Cooperation($Islets of Langerhans/*ultrastructure kinetics language languageslarge-deformationlateral diffusion Mammals Mathematics mechanismsmesenchymal condensation microarray$Microscopy, Electron, ScanningMitosis/physiologymodelModels, BiologicalModels, Molecularmolecular cell biology molecules motilitymotion analysismuscle-contraction mutants myocyte myosin-ii$nematode caenorhabditis-elegans networks Organelles/*ultrastructureOvum/cytology/metabolism parsing biological sequences pathwayspattern-formationpercolation clustersphylogenetic trees prediction proliferation protein pseudopodsRats reactants recognition recordings$ Research Support, Non-U.S. Gov't,(Research Support, U.S. Gov't, Non-P.H.S.($Research Support, U.S. Gov't, P.H.S.4/Research/*methods/organization & administrationrnarna and protein structurerna trafficking sensitivity$Signal Transduction/physiologysignaling pathway simulation simulations Skin/*surgerySocial Behaviorstate chemical-kineticsstochastic simulationStress, Mechanical surface systemssystems biologySystems Integration tensegritytheoretical-models theory Tomography, X-Ray ComputedTomography/*methods40Urothelium/cytology/drug effects/physiopathologyvertebrate limb Virginia virtual cellViscera/*physiology VisualizationWound Healing/*physiology,&Wound Healing/drug effects/*physiology4/Wounds, Penetrating/*pathology/*physiopathology4/Yeasts/cytology/growth & development/metabolismDeLisi, C. Vajda, S. 1999,&Computational problems in cell biology("Computing in Science & Engineering13R 26-32tMAY-JUNl$Comput Sci Eng Comput Sci Eng ISI:000080067500011gIeee Computer SocrHAprotein docking recognition prediction molecules complexes genome,%ObDeLisi, C. Vajda, S. 1999,&Computational problems in cell biology("Computing in Science & Engineering13R 26-32tMAY-JUNl$Comput Sci Eng Comput Sci Eng ISI:000080067500011gIeee Computer SocrHAprotein docking recognition prediction molecules complexes genome,%Obtaining a predictive understanding of cell behavior will require new computational methods, as well as adaptations of traditional techniques of optimization and system analysis. The authors discuss the challenges cell biologists face in their effort to control information transfer in cells.eSTATUS: p, h RATING: ***-- TYPE: bio, biotech COMMENT: okay, I guess Q ASKED: what challenges do modern cell biologists face ANS GIVEN: shitloads INTEREST: talks about "control circuits" in cells - interesting idea (good analogy pg 28) - but ultimately cell is more complex than electrical - also various pathways interact. Q RAISED: - CONTRIB: - EXTRA INFO: Times Cited: 0 Article English Cited References Count: 28 192fh  /69FGNHPT[`j$://000080067500011'DeLisi, C. Boston Univ, Coll Engn, Off Dean, 44 Cummington St, Boston, MA 02215 USA Boston Univ, Coll Engn, Off Dean, Boston, MA 02215 USA >& Heid, P. J. Voss, E. Soll, D. R. 20023D-DIASemb: A computer-assisted system for reconstructing and motion analyzing in 4D every cell and nucleus in a developing embryoDevelopmental Biology> 2452329-347? MAY 15Dev Biol Dev BioloISI:000175601900008t*#Academic Press Inc Elsevier ScienceI3d reconstruction motion analysis embryogenesis c. elegans nematode caenorhabditis-elegans crawling cells 3-dimensional reconstruction myosin-ii chemotaxis motility dictyostelium embryogenesis mutants pseudopodsA computer-assisted three-dimensional (3D) system, 3D-DIASemb, has been developed that allows