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Group: dIEMoSIRIS - library [543 articles]

Недавние статьи, отправленные по почте членами dIEMoSIRIS группы
  • BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.
    Bioinformatics (Oxford, England), Vol. 20, No. 17. (22 November 2004), pp. 3289-3291.
    by ML Blinov, JR Faeder, B Goldstein, WS Hlavacek
    posted to no-tag by mattis23 to the group dIEMoSIRIS on 2008-05-28 08:30:06 as ** along with 1 group MoSi-Rostock
  • SBMLmerge, a system for combining biochemical network models.
    Genome informatics. International Conference on Genome Informatics, Vol. 17, No. 1. (2006), pp. 62-71.
    by M Schulz, J Uhlendorf, E Klipp, W Liebermeister
    posted to sbmlmerge model_management model_components by dagmar to the group dIEMoSIRIS on 2008-04-23 15:06:51 as ***** along with 1 person lenov
  • The Estimation of Kinetic Parameters in Systems Biology by Comparing Molecular Interaction Fields of Enzymes
    (2006)
    by M Stein, RR Gabdoulline, B Besson, RC Wade
    posted to sabio-rk model_management by dagmar to the group dIEMoSIRIS on 2008-04-23 15:00:47 as *****
  • Fusing and Composing Macromolecular Regulatory Network Models
    (March 2007), pp. 337-344.
    by R Randhawa, CA Shaffer, JJ Tyson
    posted to model model_components by dagmar to the group dIEMoSIRIS on 2008-04-18 14:26:54 as ***** along with 1 group compneur
  • Modeling and querying biomolecular interaction networks
    Theor. Comput. Sci., Vol. 325, No. 1. (September 2004), pp. 25-44.
    by Nathalie Chabrier-Rivier, Marc Chiaverini, Vincent Danos, Fran\ccois Fages, Vincent Schächter
    posted to no-tag by mattis23 to the group dIEMoSIRIS on 2008-03-31 13:42:44 as **** along with 1 group MoSi-Rostock
  • A Spatial Extension to the [pi] Calculus
    Electronic Notes in Theoretical Computer Science, Vol. 194, No. 3. (20 January 2008), pp. 133-148.
    by Mathias John, Roland Ewald, Adelinde M Uhrmacher
    posted to no-tag by mattis23 to the group dIEMoSIRIS on 2008-03-31 13:30:56 as * along with 1 group MoSi-Rostock
  • Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch
    Transactions on Computational Systems Biology VII (2006), pp. 24-55.
    by Céline Kuttler, Joachim Niehren
    posted to no-tag by mattis23 to the group dIEMoSIRIS on 2008-03-13 19:14:04 as read along with 1 group MoSi-Rostock
  • A Stochastic Pi Calculus for Concurrent Objects
    Algebraic Biology (2007), pp. 232-246.
    by Céline Kuttler, Cédric Lhoussaine, Joachim Niehren
    posted to no-tag by mattis23 to the group dIEMoSIRIS on 2008-03-13 19:07:02 as read
  • The Petri Net Markup Language
    Petri Net Technology for Communication-Based Systems (2003), pp. 124-144.
    by Michael Weber, Ekkart Kindler
    posted to petrinets pnml by dagmar to the group dIEMoSIRIS on 2008-01-25 08:08:03 as ***** along with 1 person wnpx
  • notes The Biology Petri Net Markup Language
    by Ming Chen, Andreas Freier, Jacob Köhler, Alexander Regg
    posted to pnml by dagmar to the group dIEMoSIRIS on 2008-01-25 08:02:31 as ***** along with 1 person wnpx
  • Why most published research findings are false.
    PLoS Med, Vol. 2, No. 8. (August 2005)
    by JP Ioannidis
    posted to false-positive review by arne to the group dIEMoSIRIS on 2008-01-18 13:00:25 as read along with 37 people and 3 groups achinerarias austin rklancer jyuh phnk sebpaquet incites garyfeng monod Borelli jmeppley chad_davis Najamuddin irinas indigoviolet mwyarbro ddahlem dullhunk madhadron balabu jiyu msierk Imat lmi_swap chenlc03 biblio24 pratap OriginalLurch cjeans feipan suizan jasonbobe lonettma buggle dnugent Malc elsbury ReadingLab EisenLab Sciences_communication_societe
  • The Polyadic pi-Calculus: A Tutorial
    (1993)
    by Robin Milner
    edited by FL Hamer, W Brauer, H Schwichtenberg
    posted to pi-calculus polyadic by dagmar to the group dIEMoSIRIS on 2007-12-21 08:59:09 as **** along with 1 person Grobi
  • PML: Toward a High-Level Formal Language for Biological Systems
    Electronic Notes in Theoretical Computer Science, Vol. 180, No. 3. (18 July 2007), pp. 15-30.
    by Bor-Yuh E Chang, Manu Sridharan
    posted to ml piml xml by dagmar to the group dIEMoSIRIS on 2007-11-26 17:12:39 as **
  • Modelling Cellular Processes Using Membrane Systems with Peripheral and Integral Proteins
    Computational Methods in Systems Biology (2006), pp. 108-126.
    by Matteo Cavaliere, Sean Sedwards
    posted to simulation_tools cytosim by dagmar to the group dIEMoSIRIS on 2007-09-21 14:32:31 as **** along with 1 group compneur
  • Cyto-Sim Example Models: Oscillators
    (December 2006)
    by Sean Sedwards
    posted to simulation_tools miose lotka_volterra cytosim by dagmar to the group dIEMoSIRIS on 2007-09-21 13:52:11 as ***** along with 1 group compneur
  • Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source
    Proceedings of the National Academy of Sciences, Vol. 103, No. 2. (10 January 2006), pp. 389-394.
    by Michal Ronen, David Botstein
    posted to mrna_levels microarray hxt glucose by arne to the group dIEMoSIRIS on 2007-09-19 13:55:13 as ****
  • The Pi Markup Language
    (19 September 2007)
    by Mathias John, Dagmar Koehn, Robert Waltemath
    posted to xml_schema xml pi-calculus by dagmar to the group dIEMoSIRIS on 2007-08-30 09:05:06 as read along with 1 person and 1 group Grobi compneur
  • Data Integration in the Life Sciences: 4th International Workshop, DILS 2007, Philadelphia, PA, USA, June 27-29, 2007, Proceedings (Lecture Notes in Computer Science)
    (20 July 2007)
    edited by Sarah Cohen-Boulakia, Val Tannen
    posted to data_retrieval dataintegration database by dagmar to the group dIEMoSIRIS on 2007-08-30 08:23:10 as ** along with 1 group compneur
  • A composability lexicon
    Proceedings of the Spring 2003 Simulation Interoperability Workshop (2003), pp. 181-187.
    by MD Petty, EW Weisel
    posted to interoperability composition composability by carmaus to the group dIEMoSIRIS on 2007-08-29 16:05:54 as **** along with 1 group MoSi-Rostock
  • Towards Reusing Model Components in Systems Biology
    Computational Methods in Systems Biology (2005), pp. 192-206.
    by Adelinde M Uhrmacher, Daniela Degenring, Jens Lemcke, Mario Krahmer
    posted to xml systems_biology composition by carmaus to the group dIEMoSIRIS on 2007-08-27 13:44:43 as read along with 2 people and 2 groups dagmar csgillespie MoSi-Rostock compneur
  • Dynamic complex formation during the yeast cell cycle.
    Science, Vol. 307, No. 5710. (4 February 2005), pp. 724-727.
    by U de Lichtenberg, LJ Jensen, S Brunak, P Bork
    posted to yeast microarray cell_cycle by arne to the group dIEMoSIRIS on 2007-08-21 14:12:21 as read along with 11 people gjuggler carlk mdimmic chad_davis balajis wnpx koller massivemayhem cjeans phoenixzxl larsjuhljensen
  • OCML Ontologies to XML Schema Lowering
    (2004)
    by V Tanasescu, J Domingue, L Cabral
    posted to xml_schema transformation owl ontology by dagmar to the group dIEMoSIRIS on 2007-08-12 13:16:12 as ***** along with 1 group compneur
  • Executable biology
    (2006), pp. 1675-1682.
    by Jasmin Fisher, Thomas A Henzinger
    posted to systems-biology by roland_ewald to the group dIEMoSIRIS on 2007-08-07 17:25:25 as read along with 2 people and 2 groups wnpx dagmar MoSi-Rostock compneur
  • IntEnz, the integrated relational enzyme database.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by A Fleischmann, M Darsow, K Degtyarenko, W Fleischmann, S Boyce, KB Axelsen, A Bairoch, D Schomburg, KF Tipton, R Apweiler
    posted to intenz database by dagmar to the group dIEMoSIRIS on 2007-08-05 16:23:40 as ** along with 1 person and 1 group grottenolm compneur
  • Systems Biology Markup Language (SBML) Level 3 - Proposal: Model Composition Features
    (October 2003)
    by Andrew Finney
    posted to sbml modularity model by dagmar to the group dIEMoSIRIS on 2007-08-05 14:54:22 as read along with 1 person and 1 group wnpx compneur
  • A Universal Module Concept for Petri Nets --- an implementation-oriented approach
    Informatikberichte 150 (2001)
    by Ekkart Kindler, Michael Weber
    posted to transformation sbml petri_nets by dagmar to the group dIEMoSIRIS on 2007-08-05 10:41:25 as ***** along with 1 group compneur
  • Mathematical and computational techniques to deduce complex biochemical reaction mechanisms.
    Progress in Biophysics and Molecular Biology, Vol. 86, No. 1. (September 2004), pp. 77-112.
    by EJ Crampin, S Schnell, PE Mcsharry
    posted to ode by dagmar to the group dIEMoSIRIS on 2007-08-04 15:14:05 as ** along with 3 people and 3 groups alexr aheilbut schnell Autoregulation IU_Informatics_CX compneur
  • A Specification Language and a Framework for the Execution of Composite Models in Systems Biology
    Lecture Notes In Computer Science:Transactions on Computational Systems Biology VII, Vol. 4230 (2006), pp. 163-184.
    by Ofer Margoninski, Peter Saffrey, James Hetherington, Anthony Finkelstein, Anne Warner
    posted to xml systems_biology modularity modeling composition by carmaus to the group dIEMoSIRIS on 2007-08-03 08:46:51 as read along with 3 people and 2 groups wnpx krissp dagmar MoSi-Rostock compneur
  • Flexible integration of XML into modeling and simulation systems
    (December 2005), pp. 1813-1820.
    by Mathias Röhl, Adelinde M Uhrmacher
    edited by ME Kuhl, NM Steiger, FB Armstrong, JA Joines
    posted to xml_schema model_formalisms integration devs by dagmar to the group dIEMoSIRIS on 2007-08-02 14:21:36 as ***** along with 1 person and 1 group wnpx compneur
  • A Multi-Formalism Modeling Composability Framework: Agent and Discrete-Event Models
    (2005), pp. 249-256.
    by Hessam Sarjoughian, Dongping Huang
    posted to multi-formalism modularity modeling composition agents by carmaus to the group dIEMoSIRIS on 2007-08-02 08:31:14 as read along with 1 person and 1 group krissp MoSi-Rostock
  • The Petri Net Markup Language: Concepts, Technology, and Tools
    Applications and Theory of Petri Nets 2003: 24th International Conference, ICATPN 2003, Eindhoven, The Netherlands, June 23-27, 2003. Proceedings (June 2003), pp. 1023-1024.
    by Jonathan Billington, Søren Christensen, Kees van Hee, Ekkart Kindler, Olaf Kummer, Laure Petrucci, Reinier Post, Christian Stehno, Michael Weber
    posted to transformation pnml petri_nets by dagmar to the group dIEMoSIRIS on 2007-08-01 15:41:45 as ***** along with 1 group compneur
  • Addressing the challenges of multiscale model management in systems biology
    Computers & Chemical Engineering, Vol. 31, No. 8. (15 August 2007), pp. 962-979.
    by J Hetherington, IDL Bogle, P Saffrey, O Margoninski, L Li, Varela M Rey, S Yamaji, S Baigent, J Ashmore, K Page, RM Seymour, A Finkelstein, A Warner
    posted to multi-scale model_management model by carmaus to the group dIEMoSIRIS on 2007-08-01 10:43:48 as ** along with 1 person and 2 groups dagmar MoSi-Rostock compneur
  • An Overview of CellML 1.1, a Biological Model Description Language
    SIMULATION, Vol. 79, No. 12. (1 December 2003), pp. 740-747.
    by Autumn A Cuellar, Catherine M Lloyd, Poul F Nielsen, David P Bullivant, David P Nickerson, Peter J Hunter
    posted to cellml by dagmar to the group dIEMoSIRIS on 2007-08-01 09:38:45 as **** along with 1 person and 1 group petergun6666 compneur
  • CellML: its future, present and past
    Progress in Biophysics and Molecular Biology, Vol. 85, No. 2-3. ( 2004), pp. 433-450.
    by Catherine M Lloyd, Matt D Halstead, Poul F Nielsen
    posted to model_management modelling model cellml by dagmar to the group dIEMoSIRIS on 2007-08-01 09:09:33 as ***** along with 2 people and 1 group csanford lenov compneur
  • Agreeing to Disagree
    The Annals of Statistics, Vol. 4, No. 6. (1976), pp. 1236-1239.
    by Robert J Aumann
    posted to game_theory by arne to the group dIEMoSIRIS on 2007-07-31 12:48:00 as *** along with 1 person toomash
  • A new framework for the integration of models in biology
    (2004)
    by R Wright, Varela, O Margoninski, P Saffrey, J Hetherington, L Li, R Seymour, A Warner, A Finkelstein
    posted to sb model integration by dagmar to the group dIEMoSIRIS on 2007-07-31 10:54:43 as **** along with 1 group compneur
  • Robust global sensitivity in multiple enzyme cascade system explains how the downstream cascade structure may remain unaffected by cross-talk.
    FEBS Lett, Vol. 558, No. 1-3. (30 January 2004), pp. 79-84.
    by VK Mutalik, AP Singh, JS Edwards, KV Venkatesh
    posted to cascades by arne to the group dIEMoSIRIS on 2007-07-31 08:47:40 as read
  • Alternative signaling pathways: When, where and why?
    FEBS Letters, Vol. 579, No. 24. (10 October 2005), pp. 5265-5274.
    by Yunchen Gong, Zhaolei Zhang
    posted to specificity signaling by carmaus to the group dIEMoSIRIS on 2007-07-31 08:08:05 as ** along with 1 person and 1 group arne MoSi-Rostock
  • Combining Micro and Macro-Modeling in DEVS for Computational Biology
    (December 2007)
    by Adelinde M Uhrmacher, Roland Ewald, Mathias John, Carsten Maus, Matthias Jeschke, Susanne Biermann
    posted to multi-scale modelling model_formalisms by dagmar to the group dIEMoSIRIS on 2007-07-30 14:22:20 as ***** along with 1 group compneur
  • Model composability: formulating a research thrust: composable simulations
    (2000), pp. 1577-1584.
    by Stephen Kasputis, Henry C Ng
    posted to simulation modularity modeling composition by carmaus to the group dIEMoSIRIS on 2007-07-30 09:09:33 as ** along with 2 people and 1 group krissp Scis0000002 MoSi-Rostock
  • Architectural mismatch or why it's hard to build systems out of existing parts
    (1995), pp. 179-185.
    by David Garlan, Robert Allen, John Ockerbloom
    posted to modularity engineering composition by carmaus to the group dIEMoSIRIS on 2007-07-30 09:03:07 as ** along with 11 people and 2 groups ingstrup hamish lfk jolilius fachri bfraser ddahlem krissp RalfMitschke buchgeher gvdh TUCS-ES_Lab MoSi-Rostock
  • Stochastic simulation of chemical kinetics.
    Annu Rev Phys Chem, Vol. 58 (2007), pp. 35-55.
    by DT Gillespie
    posted to tau-leaping stiff_systems master_equation langevin_equation by carmaus to the group dIEMoSIRIS on 2007-07-30 08:29:59 as ** along with 3 people and 2 groups jjray dbikard pmendes Centre de Recherches Interdisciplinaires MoSi-Rostock
  • Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.
    Curr Opin Cell Biol, Vol. 15, No. 2. (April 2003), pp. 221-231.
    by JJ Tyson, KC Chen, B Novak
    posted to pathways ode modularity dynamic by carmaus to the group dIEMoSIRIS on 2007-07-30 07:44:18 as ** along with 5 people and 4 groups camster rklancer monod rhem1224 bayesian dbk-lab TCR_Signaling SysbioMPI-TCells MoSi-Rostock
  • ALIBABA: PubMed as a graph
    Bioinformatics, Vol. 22, No. 19. (1 October 2006), pp. 2444-2445.
    by Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jorg Hakenberg, Ulf Leser
    posted to tool pubmed data_retrieval data_mining by dagmar to the group dIEMoSIRIS on 2007-07-27 11:55:18 as read along with 4 people and 1 group jyuh ianturton avivagabriel A_Hoogendam compneur
  • OntoDB: It is Time to Embed your Domain Ontology in your Database
    (2007)
    by Stéphane Jean, Hondjack Dehainsala, Dung N Xuan, Guy Pierra, Ladjel Bellatreche, Yamine Aït-Ameur
    posted to sb ontology database by dagmar to the group dIEMoSIRIS on 2007-07-27 11:52:57 as ** along with 1 person and 1 group stephane-jean compneur
  • The Relation between Ontologies and Schema-languages: Translating OIL-specifications in XML-Schema
    (2000)
    by M Klein, D Fensel, F van Harmelen, I Horrocks
    posted to xml_schema transformation ontology by dagmar to the group dIEMoSIRIS on 2007-07-27 11:33:14 as ***** along with 3 people and 3 groups maripsa wcrosbie anansi Wikipedia CoP_CMS compneur
  • Theory of Modeling and Simulation
    (10 January 2000)
    by Bernard P Zeigler, Tag G Kim, Herbert Praehofer
    posted to modelling devs by dagmar to the group dIEMoSIRIS on 2007-07-26 08:28:02 as **** along with 5 people and 2 groups lop cedricboidin harald carmaus mingguo SIG compneur
  • little b - a language for modular, shareable models of biological systems
    (2004)
    by A Mallavarapu, J Gunawardena
    posted to virtual_cell modularity littleb by carmaus to the group dIEMoSIRIS on 2007-07-25 16:42:13 as read along with 1 group MoSi-Rostock
  • Systems biology: its practice and challenges.
    Cell, Vol. 121, No. 4. (20 May 2005), pp. 511-513.
    by A Aderem
    posted to systems_biology modularity commentary by carmaus to the group dIEMoSIRIS on 2007-07-25 12:46:13 as read along with 3 people and 1 group LeightonP wnpx biosv MoSi-Rostock
  • Discrete event modelling and simulation in systems biology
    Journal of Simulation, Vol. 1 (2007), pp. 81-96.
    by Roland Ewald, Carsten Maus, Arndt Rolfs, Adelinde Uhrmacher
    posted to modelling model_formalisms model by dagmar to the group dIEMoSIRIS on 2007-07-25 10:49:28 as ***** along with 1 person and 1 group carmaus compneur
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