Composable languages for bioinformatics: the NYoSh experiment by Manuele Simi, Fabien Campagne. (Simi M, Campagne F. (2014) Composable languages for bioinformatics: the NYoSh experiment. PeerJ 2:e241 http://dx.doi.org/10.7717/peerj.241)
Abstract:
Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is distributed at http://nyosh.campagnelab.org.
In the discussion section of the paper the authors concede:
We expect that widespread use of LWB will result in a multiplication of small languages, but in a manner that will increase language reuse and interoperability, rather than in the historical language fragmentation that has been observed with traditional language technology.
Whenever I hear projections about the development of languages I am reminded the inventors of “SCSI” thought it should be pronounced “sexy,” whereas others preferred “scuzzi.” Doesn’t have the same ring to it does it?
I am all in favor of domain specific languages (DSLs), but at the same time, am mindful that undocumented languages are in danger of becoming “dead” languages.
Agree that a challenge is documentation of the multiple languages offered by language workbenches. Took a crack at it writing a book about the MPS language platform. See http://campagnelab.org/our-books/
There are many languages, but most are small and can be quickly described.
The sum of documentation is similar to that of any of the traditional programming languages already in existence. The difference is that you need to document (or learn) just a small bit in incremental manner each time a new language is offered on the platform.
Comment by campagne — March 12, 2014 @ 7:47 am