PhyloclassTalk (was: Re: [squeak-dev] [ANN] BioSqueak 0.4)
Hello Hannes, Sorry for the late response, I have been working intensively in an application using BioSmalltalk. Here is a post with some screenshots: http://biosmalltalk.blogspot.com.ar/2013/02/phyloclasstalk-preview.html as I've said, it is developed in Pharo but most subsystems work in Squeak too. I cross-post to the Pharo users list in case someone is interested. El 16/02/2013 16:00, H. Hirzel escribió:
Hello Hernán
Thank you for your elaboration on the topic of BioSqueak.
On 2/1/13, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hello Hannes, Thanks for the feedback! Some answers then between the lines:
El 01/02/2013 11:35, H. Hirzel escribió:
Hello Hernán
This is interesting. http://biosmalltalk.blogspot.com/
I understand that you have constructed an internal domain specific language (a DSL, a query language) for dealing with genetic data in Smalltalk
search := BioNCBIWWWBlastClient new nucleotide query: 'CCCTCAAACAT...TTTGAGGAG'; hitListSize: 150; filterLowComplexity; expectValue: 10; wordSize: 11; blastn; blastPlainService; alignmentViewFlatQueryAnchored; formatTypeXML; fetch. search outputToFile: 'blast-query-result.xml' contents: search result.
Is there a description of this DSL?
Is not a DSL in the traditional sense, i.e., using ANTLR, Lex or Yacc, but a "DSL" which is embedded thus inheriting the syntax and execution semantics of Smalltalk.
Yes, I understand, the regular thing in Smalltalk as every Smalltalk domain model could be considered a DSL to a certain extent/
Lukas Renggli has a useful classification on DSLs in his PhD dissertation on 'Dynamic Language Embedding'' http://scg.unibe.ch/archive/phd/renggli-phd.pdf Chapter 2
According to that you probably have an Internal DSL (chapter 2.1), right?
Yes, it would fit into the Internal DSL category. I didn't knew about that classification, thanks for sharing.
To clarify: I've not built a DSL specification for the QBlast API, although I'm willing to develop DSLs for bioinformatics APIs in a Smalltalk language workbench (anyone?).
OK
Currently the messages for performing alignments at the NCBI are based in the API specification, http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html .
The unary
sends are the result of a plan to reduce parametrization and to replicate or customize Blast settings through a UI. This is because geneticists experiment changing Blast parameters over time and I want my system not to be tied to textual parameters.
The data is kept in XML files and all is read into the image to be queried. It seems that you don't have a problem with the image size?
Yes I had problems with image size and performance, a lot indeed.
Actually working with XML DOM with alignments of 5000 or more hits Squeak (and Pharo of course) started to show slowliness. So I cannot keep all XML nodes in memory. To overcome this problem I've tried the SAX (push) parser and the XMLPullParser (which is a StAX parser). Then my idea was to reduce the tree by specifying only the XML nodes which I'm interested for. After reducing the nodes, I wrote custom XML tree classes with a specific API to query blast XML results, taken form the DTD specification. AFAIK this is known as a XML digester, which is somewhat "evolved" in Java (http://commons.apache.org/digester/xmlrules.html).
I understand that you took http://www.squeaksource.com/XMLSupport/ (the XML support repo for Pharo, for Squeak XML support is in the trunk image) and modified it.
I have built a dynamic query builder in Morphic for querying the XML providing the possibility of persist and update the filters. Unfortunately for Squeak users I'm using the Polymorph API, which I think is not available in Squeak.
A screen shot would be appreciated... :-)
Ok, the blog post includes some screenshots.
We worked using the XML push/pull parsers for reading genomes and they worked acceptably. But it is impossible to keep nodes for 3 GBytes of XML at least for now in Squeak/Pharo.
According to my experience keeping XML structures in the image is inefficient in terms of memory usage. More efficient ways are needed and XML is then only for reading/writing to external files.
Exactly, XML is not good at all for big data.
More and critical problems arise when trying to work with microarray data (big data) in Smalltalk which is not document-oriented. I had to switch to "solutions" like SQL, or HDF5 using Pytables with well-designed scheme for our input. The advantages are that supports indexing and reading data in blocks, besides tools like Vitables or HDFView to navigate the data. Until someone provides some bits in this field, there is little opportunity for using Smalltalk.
But what I understand is that people keep DNA data in memory for speed reasons and use C++ or Perl programs to deal with it.
It really depends of the type of analysis, I've seen most starter bioinformaticians prefer Python over Perl because of the nicer syntax and more complete library support. I don't know big data projects using C++ with raw DNA data. Compression with indexing, and specialized file formats are used these days, splitting data in clusters where needed. I would love to see some Smalltalkers working on dataspaces too. See these presentations: http://www.slideshare.net/mndoci/presentations
I would welcome a short writeup with a general introduction to what you are doing in http://biosmalltalk.blogspot.com/.
We have submitted a paper recently and we are waiting for the review results. On the other side we are preparing another paper for a phylogenetics decision support system which includes text-mining and a rule engine. I will try to write an entry in the next week with screenshots.
Any news on this?
No news so far, still in the reviewing process. Best regards, Hernán
Kind regards Hannes
Best regards,
Hernán
Kind regards
Hannes Hirzel
On 2/1/13, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hi,
Few days ago I created a port of BioSmalltalk for Squeak too. BioSmalltalk is a library for doing Bioinformatics with Smalltalk. This port is labelled "BioSqueak" and I expect to release a version for Windows sometime soon. You can find it in:
http://code.google.com/p/biosmalltalk/downloads/list
I'm very interested in feedback. Thanks for reading.
Hernán
-- Hernán Morales Institute of Veterinary Genetics (IGEVET) http://igevet.fcv.unlp.edu.ar National Scientific and Technical Research Council (CONICET). La Plata (1900), Buenos Aires, Argentina. Telephone: +54 (0221) 421-1799. Internal: 422 Fax: 425-7980 or 421-1799.
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Hernán Morales Durand