Re: [cellml-discussion] little b - shared models built from reusable parts
My own $0.02, as another software developer and an old Lisp hacker myself (and of course, everything I say here is purely personal opinion). TY I think this can be done with a programming language. Yup, you can exchange programs as your model description, and people did essentially that for a few decades. (They still do even today, especially when the model is, e.g., MATLAB code.) There are at least two reasons why people are trying to move away from that: 1) The system interpreting the description must implement the entire programming language interpreter. Little b, for example, needs Lisp underneath it. But regardless of whether your description requires Lisp or not, it's a nontrivial requirement. It reduces your ability to share the model on the one hand, and the size of your willing audience on the other. 2) The essence of what you're trying to model becomes lost. It is no longer a description of the domain phenomena (here, biological mechanisms), and instead becomes tied up with artifacts of the simulation/analysis framework. (I'm sorry if that seems obvious and I'm missing your point!) TY XML based languages have other types of advantages TY over lisp-based languages, naming the great number of TY tools able to interpret XML files, interoperability TY with XML/RDF for a variety of metadata capabilities, TY and many more. I'm not sure if you're saying this, but just to be clear, XML is *not* a programming language. It's merely a serialization format. One could use ASN.1, or Google's Protocol Buffers, or any of another of others. MH ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] little b - shared models built from reusable parts
The SBML community has know little b for a while since they first came to us, a long time ago, saying roughly we're much better than you, and we do everything in a simpler way, understandable by users. I think (and this is a personal opinion, that does NOT reflect the opinion of the SBML editors as a whole) this is a worthwhile effort, but completely different than SBML and CellML. 1) In general, the terser a language is, the more fuzzy but the harder to interpret it is. If the SBML spec is so long and complicated, it is because one of our goal is to ensure that everyone interpret an SBML description exactly the same way. That bears a lot of consequences on units etc. Terse is good. Unambiguous is better (if you want to exchange and integrate) 2) I am not sure LISP is a good *description* language. And we need to separate description of the model structure from description of the simulation. SBML and CellML are not programming language. Again this is a personal feeling. At the end I guess the only criteria is the usefullness for the scientific community. Hi all, Has anyone encountered this before? http://www.littleb.org/ The little b project is an effort to provide an open source http://www.opensource.org/ language which allows scientists to build mathematical models http://en.wikipedia.org/wiki/Mathematical_model of complex systems. The initial focus is systems biology http://en.wikipedia.org/wiki/Systems_biology. The goal is to stimulate widespread sharing and reuse of models. The little b language is designed to allow biologists to build models quickly and easily from shared parts, and to allow theorists to program new ways of describing complex systems. Currently, libraries have been developed for building ODE http://en.wikipedia.org/wiki/Differential_equation models of molecular networks in multi-compartment systems such as cellular epithelia. Little b is based in Common Lisp and contains mechanisms for rule-based reasoning, symbolic mathematics and object-oriented definitions. The syntax is designed to be terse and human-readable to facilitate communication. The environment is both interactive and compilable. Kind regards, James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074 http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:[EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] little b - shared models built from reusable parts
Nicolas Le Novere wrote: The SBML community has know little b for a while since they first came to us, a long time ago, saying roughly we're much better than you, and we do everything in a simpler way, understandable by users. I think (and this is a personal opinion, that does NOT reflect the opinion of the SBML editors as a whole) this is a worthwhile effort, but completely different than SBML and CellML. 1) In general, the terser a language is, the more fuzzy but the harder to interpret it is. If the SBML spec is so long and complicated, it is because one of our goal is to ensure that everyone interpret an SBML description exactly the same way. That bears a lot of consequences on units etc. Terse is good. Unambiguous is better (if you want to exchange and integrate) Software code can also be terse and unambiguous, and can be exchanged with others to be integrated into one's software. A software language must also be interpreted the exact same way between different interpreters, or users are not going to be interested in using the non-standard interpreters (usually, anyway). I can see the same objectives accomplished with little b just as well, provided that the model code was written with unambiguity in mind. 2) I am not sure LISP is a good *description* language. And we need to separate description of the model structure from description of the simulation. SBML and CellML are not programming language. I think this can be done with a programming language. A modeler could define a set of files as the description of the model structure, and build a different set of files for the description of the simulation, then the completed models can be assembled together. Naturally, SBML and CellML were never meant to be programming languages from the beginning. XML based languages have other types of advantages over lisp-based languages, naming the great number of tools able to interpret XML files, interoperability with XML/RDF for a variety of metadata capabilities, and many more. I see it as a case of two different class of langauges with different objectives in mind... Again this is a personal feeling. At the end I guess the only criteria is the usefullness for the scientific community. ... and both types will have their niche where they will be widely used in the community. Just a couple cents from a software programmer. Tommy. Hi all, Has anyone encountered this before? http://www.littleb.org/ The little b project is an effort to provide an open source http://www.opensource.org/ language which allows scientists to build mathematical models http://en.wikipedia.org/wiki/Mathematical_model of complex systems. The initial focus is systems biology http://en.wikipedia.org/wiki/Systems_biology. The goal is to stimulate widespread sharing and reuse of models. The little b language is designed to allow biologists to build models quickly and easily from shared parts, and to allow theorists to program new ways of describing complex systems. Currently, libraries have been developed for building ODE http://en.wikipedia.org/wiki/Differential_equation models of molecular networks in multi-compartment systems such as cellular epithelia. Little b is based in Common Lisp and contains mechanisms for rule-based reasoning, symbolic mathematics and object-oriented definitions. The syntax is designed to be terse and human-readable to facilitate communication. The environment is both interactive and compilable. Kind regards, James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] little b - shared models built from reusable parts
Hi all, Has anyone encountered this before? http://www.littleb.org/ The little b project is an effort to provide an open source http://www.opensource.org/ language which allows scientists to build mathematical models http://en.wikipedia.org/wiki/Mathematical_model of complex systems. The initial focus is systems biology http://en.wikipedia.org/wiki/Systems_biology. The goal is to stimulate widespread sharing and reuse of models. The little b language is designed to allow biologists to build models quickly and easily from shared parts, and to allow theorists to program new ways of describing complex systems. Currently, libraries have been developed for building ODE http://en.wikipedia.org/wiki/Differential_equation models of molecular networks in multi-compartment systems such as cellular epithelia. Little b is based in Common Lisp and contains mechanisms for rule-based reasoning, symbolic mathematics and object-oriented definitions. The syntax is designed to be terse and human-readable to facilitate communication. The environment is both interactive and compilable. Kind regards, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
