Software

The lab’s research is helped by the strong commitment in developing new tools.

Adun

Adun is a new extendible molecular simulation program that also includes data management and analysis capabilities. The Adun molecular simulation application has been designed from the ground up to cater for a broad range of users and needs, from computational chemists to experimental biologists. Adun provides advanced algorithms and protocols for molecular simulation which can be accessed from an intuitive user interface but also from a more flexible programmatic level. It is built on the Adun framework which is a powerful library for creating and manipulating simulations. However it goes beyond just performing simulations by incorporating tools for analysis and management of simulation data aswell as providing mechanisms that allow the easy extension of its abilities. In many senses Adun is simply a structure that can incorporate any molecular simulation tools allowing it almost unlimited potential for growth.

• [2011,article] bibtex
  C. Ávila, N. Drechsel, R. Alcántara, and J. Villà-Freixa, "Multiscale Simulations of Protein Aggregation," Curr. Prot. Pept. Sci., vol. 12, pp. 221-234, 2011.
  @ARTICLE{Avila2011,
  author = {C\'esar \'Avila and Nils Drechsel and Ra\'ul Alc\'antara and Jordi Vill\`a-Freixa},
  title = {{Multiscale Simulations of Protein Aggregation}},
  journal = {Curr. Prot. Pept. Sci.},
  year = {2011},
  volume = {12},
  pages = {221--234},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/21348836}
}

• [2009,phdthesis] bibtex
  M. A. Johnston, "Development of a Molecular Simulator and its Application to Conformational Changes in Biomolecules," PhD Thesis , 2009.
  @PHDTHESIS{Johnston2009,
  author = {Johnston, M. A.},
  title = {{Development of a Molecular Simulator and its Application to Conformational Changes in Biomolecules}},
  school = {Universitat Pompeu Fabra},
  year = {2009},
  abstract = {This thesis deals with the creation of a new open-source program and API for biomolecular simulation and its subsequent application to biological problems. The program, Adun, focuses on the key areas of biological free-energy calculations, rapid development and high-performance productivity. Methods such as SCAAS, EVB and switched Generalised-Born have been implemented to realise the first aim. The presence of these techniques, along with a multitude of others, verifies Adun's rapid development potential. All these features are united by an advanced graphical user interface which provides novel capabibilities such as inbuilt data management, and distributed datasharing and computation. Adun's ability to tackle biological problems is illustrated with an investigation of Ras dynamics and the development, implementation and testing of a novel method for determining transition paths. In addition to concretely demonstrating Adun's potential these studies also provide insight into the use of dynamic information in elucidating protein function. The current state of the program and the results of the two studies is discussed and indications of future aims and directions given. In addition personal thoughts on the role of computational biologists as developers of applications, for themselves and the wider scientific community, are provided},
  url = {http://www.tesisenxarxa.net/TDX-1015109-103730/}
}

• [2007,article] bibtex
  M. A. Johnston and J. Villà-Freixa, "Enabling Data Sharing and Collaboration in Complex Systems Applications," LNBI, vol. 4360, pp. 124-140, 2007.
  @ARTICLE{Johnston2007,
  author = {Johnston, M.A. and Vill\`a-Freixa, J.},
  title = {{Enabling Data Sharing and Collaboration in Complex Systems Applications}},
  journal = LNBI, year = {2007},
  volume = {4360},
  pages = {124--140},
  timestamp = {2008.12.02},
  url = {http://www.springerlink.com/content/9476700461j37732}
}

• [2005,article] bibtex
  M. A. Johnston, I. F. Galván, and J. Villà-Freixa, "Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.," J Comput Chem, vol. 26, iss. 15, pp. 1647-1659, 2005.
  @ARTICLE{Johnston2005b,
  author = {Michael A Johnston and Ignacio Fdez Galv\'an and Jordi Vill\`a-Freixa},
  title = {Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.},
  journal = {J Comput Chem},
  year = {2005},
  volume = {26},
  pages = {1647--1659},
  number = {15},
  month = {Nov},
  abstract = {Here we present Adun, a new molecular simulator that represents a paradigm shift in the way scientific programs are developed. The traditional algorithm centric methods of scientific programming can lead to major maintainability and productivity problems when developing large complex programs. These problems have long been recognized by computer scientists; however, the ideas and techniques developed to deal with them have not achieved widespread adoption in the scientific community. Adun is the result of the application of these ideas, including pervasive polymorphism, evolutionary frameworks, and refactoring, to the molecular simulation domain. The simulator itself is underpinned by the Adun Framework, which separates the structure of the program from any underlying algorithms, thus giving a completely reusable design. The aims are twofold. The first is to provide a platform for rapid development and implementation of different simulation types and algorithms. The second is to decrease the learning barrier for new developers by providing a rigorous and well-defined structure. We present some examples on the use of Adun by performing simple free-energy simulations for the adiabatic charging of a single ion, using both free-energy perturbation and the Bennett's method. We also illustrate the power of the design by detailing the ease with which ASEP/MD, an elaborated mean field QM/MM method originally written in FORTRAN 90, was implemented into Adun.},
  doi = {10.1002/jcc.20312},
  institution = {Computational Biochemistry and Biophysics Laboratory, Research Group on Biomedical Informatics (GRIB), Institut Municipal d'Investigaci� M�dica and Universitat Pompeu Fabra, C/Doctor Aiguader, 80 08003 Barcelona, Catalunya, Spain.},
  keywords = {Algorithms; Computer Simulation; Equipment Design; Models, Chemical; Software},
  owner = {jordivilla},
  pmid = {16175583},
  timestamp = {2010.03.14},
  url = {http://dx.doi.org/10.1002/jcc.20312}
}

ByoDyn

In systems biology it is becoming a routine task to build models of increasing complexity on a given biochemical network or pathway of interest. One of the main problems in building such models is the determination of the parameters underlying each modelled process. ByoDyn has been designed to provide an easily extendable computational framework to estimate and analyze parameters in highly uncharacterized models.

• [2008,article] bibtex
  L. G. A. de Lomana, À. Gómez-Garrido, D. Sportouch, and J. Villà-Freixa, "Optimal Experimental Design in the Modelling of Pattern Formation," LNCS, vol. 5101, pp. 610-619, 2008.
  @ARTICLE{Lomana2008,
  author = {A. L\'{o}pez Garc\'{i}a de Lomana and \`{A}. G\'{o}mez-Garrido and D. Sportouch and J. Vill\`{a}-Freixa},
  title = {Optimal Experimental Design in the Modelling of Pattern Formation},
  journal = {LNCS},
  year = {2008},
  volume = {5101},
  pages = {610-619},
  url = {http://www.springerlink.com/content/kk7774170666m254/fulltext.pdf}
}

MIPSim

MIPSim (Molecular Interaction Potential Similarity) is a computer package that calculates both quantum and classical MIPs of biomolecules and makes comparisons and superpositions based on them. The program is opensource although its development is currently discontinued in the lab. More efforts will be done in the (near?) future

• [2005,misc] bibtex
  M. Barbany, M. de Cáceres, J. J. Lozano, J. Villà, and F. Sanz, MIPSIM: molecular interaction potential similarity analysisIMIM Hospital del Mar, 2005.
  @MISC{Barbany2005,
  author = {Montserrat Barbany and Miquel de C\'aceres and Juan Jos\'e Lozano and Jordi Vill\`a and Ferran Sanz},
  title = {MIPSIM: molecular interaction potential similarity analysis},
  year = {2005},
  publisher = {IMIM Hospital del Mar},
  url = {https://sourceforge.net/projects/mipsim/}
}

• [2002,incollection] bibtex
  F. Sanz, M. de Cáceres, and J. Villà, "Similarity analysis of Molecular Interaction Potential Distributions: The MIPSIM software," , Carbó-Dorca, R., Ed., Kluwer Academic, 2002.
  @INCOLLECTION{Sanz2002,
  author = {Sanz, F. and de C\'aceres, M. and Vill\`a, J.},
  title = {{Similarity analysis of Molecular Interaction Potential Distributions: The MIPSIM software}},
  booktitle = {{The Fundamentals of Molecular Similarity}},
  publisher = {Kluwer Academic},
  year = {2002},
  editor = {Carb\'o-Dorca, R.},
  timestamp = {2008.12.02}
}

• [2000,article] bibtex
  M. de Cáceres, J. Villà, J. J. Lozano, and F. Sanz, "MIPSIM: similarity analysis of molecular interaction potentials," Bioinformatics, vol. 16, iss. 6, pp. 568-569, 2000.
  @ARTICLE{Caceres2000,
  author = {Miquel de C\'aceres and Jordi Vill\`a and Juan J. Lozano and Ferran Sanz},
  title = {{MIPSIM: similarity analysis of molecular interaction potentials}},
  journal = {Bioinformatics},
  year = {2000},
  volume = {16},
  pages = {568-569},
  number = {6},
  abstract = {Summary: MIPSIM is a computational package designed to analyse and compare 3D distributions of molecular interaction potentials (MIP) of series of biomolecules. Availability: MIPSIM software is freely distributed to non-profit academic institutions through its web site: http://www1.imim.es/mipsim. Other organizations must contact the developers. GAMESS (http://www.msg.ameslab.gov/GAMESS/GAMESS.html) and GRID (peter@biop.ox.ac.uk) are external software required to perform some of the MIPSIM computations. They are obtained under conditions similar to MIPSIM's. Contact: mipsim@imim.es},
  doi = {10.1093/bioinformatics/16.6.568},
  eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/16/6/568.pdf},
  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/6/568}
}

Other software

Extensive work has been also carried out in a number of software tools for computational chemistry.

• MC-TINKERRATE: a program for multiconfigurational molecular mechanics.
  • [2009,misc] bibtex
    T. V. Albu, O. Tishchenko, J. C. Corchado, Y. Kim, J. Villà, J. Xing, H. Lin, M. Higashi, and D. G. Truhlar, MC-TINKERATE 2008University of Minnesota, 2009.
    @MISC{Albu2009,
  author = {Titus V. Albu and Oksana Tishchenko and Jos\'e C. Corchado and Yongho Kim and Jordi Vill\`a and Jinhua Xing and Hai Lin and Masahiro Higashi and Donald G. Truhlar},
  title = {{MC-TINKERATE 2008}},
  year = {2009},
  publisher = {University of Minnesota},
  url = {http://comp.chem.umn.edu/mc-tinkerate/}
}
• POLYRATE: a program for variational transition state theory (VTSTS) calculations.
  • [2009,misc] bibtex
    J. Zheng, S. Zhang, B. J. Lynch, J. Corchado, Y. Chuang, P. L. Fast, W. Hu, Y. Liu, G. C. Lynch, K. A. Nguyen, C. F. Jackels, A. F. Ramos, B. A. Ellingson, V. S. Melissas, J. Villà, I. Rossi, E. L. Coitiño, J. Pu, T. V. Albu, R. Steckler, B. C. Garrett, A. D. Isaacson, and D. G. Truhlar, POLYRATE 2008: Computer Program for the Calculation of Chemical Reaction Rates for PolyatomicsUniversity of Minnesota, 2009.
    @MISC{Zheng2008,
  author = { Jingjing Zheng and Shuxia Zhang and Benjamin J. Lynch and Jos� C. Corchado and Yao-Yuan Chuang and Patton L. Fast and Wei-Ping Hu and Yi-Ping Liu and Gillian C. Lynch and Kiet A. Nguyen and Charles F. Jackels and Antonio Fernandez Ramos and Benjamin A. Ellingson and Vasilios S. Melissas and Jordi Vill\`a and Ivan Rossi and Elena L. Coiti\~no and Jingzhi Pu and Titus V. Albu and Rozeanne Steckler and Bruce C. Garrett and Alan D. Isaacson and Donald G. Truhlar},
  title = {{POLYRATE 2008: Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics}},
  year = {2009},
  publisher = {University of Minnesota},
  url = {http://comp.chem.umn.edu/polyrate/}
}
• MOLARIS: a computational biochemistry tool for the study of energetics and dynamics of proteins. Check the theory and reference manuals of the program by accessing the following links:
  • THEORY
  • REFERENCE
  • [2003,misc] bibtex
    Z. T. Chu, J. Villà-Freixa, M. v Strajbl, C. N. Schutz, A. Shurki, and A. Warshel, MOLARIS version alpha9.06.01University of Southern California, 2003.
    @MISC{Chu2003,
  author = {Chu, Z. T. and Vill\`a-Freixa, J. and {\v S}trajbl, M. and Schutz, C. N. and Shurki, A. and Warshel, A.},
  title = {{MOLARIS version alpha9.06.01}},
  year = {2003},
  date-modified = {2007-10-15 11:52:30 +0200},
  owner = {macbook},
  publisher = {University of Southern California},
  timestamp = {2008.08.14},
  url = {http://futura.usc.edu/programs/index.html}
}

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