Re: Isoelectric point and molecular weight calculations with BioJava
Peter Troshin <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Dear M. Rehan, I am happy to hear that you'd like to take my idea forward and I wish you the best of luck with your GSoC application. However please bear in mind that 1) OBF may not be accepted as a mentor organisation this year 2) my idea may not be funded even if the OBF will be accepted as a mentor organisation. 3) You as a student may not be accepted by Google (you have to make an application to them on your own) 4) You may not be the best candidate for the project 5) I have no say for the most of the above. I will be happy to have your as a student once we get to this stage but I feel that right now any requests for the supervision is a little preliminary. You can find out how to apply to GSoC here: http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs Best of luck, Peter On 08/03/2011 13:54, M. Rehan Shaukat wrote: > Dear Peter, > > After participating in Google SoC 2010 last year I am looking forward > to participate again in SoC 2011. I was following this thread > regarding the "Amino acids physico-chemical properties calculation" > idea and I also read the details of GSoC page for this project idea. > This idea sounds very interesting to me and also matches my interests > and experience (Optimisation, Multi-threading, High Performance > Computing). I have passion for work and contribute in open source > projects. I am linked with Medical Research Council (Harwell, UK) and > contributing to Europhenome <http://www.europhenome.org/> (An open > source system for handling large datasets and analysing as well as > annotating mouse phenotyping data) and EUMODIC > <http://www.eumodic.org/> projects in collaboration with HMGU, > Germany; ICS, France;and the Sanger Institute, UK. > > During my Masters thesis, I worked on a project: "Using Cell > Processors to Speed up Phylogenetic Inference" that aimed on > optimising a compute-intensive Bioinformatics application on Cell > Broadband Engine using IBM Cell Broadband Engine SDK and MPI. I have > over 4 years of research+industrial software development experience. I > have worked on different programming languages (mainly: Java, C/C++, > PHP, XML) and variety of tools and frameworks (J2EE, JUnit, Hibernate, > Spring, JMS, JMX, CORBA, RMI, Eclipse, Netbeans, SVN, CVS and more). > > I am interested in working on this project under your supervision. I > have plenty of similar experience and would be grateful for your kind > supervision. > > Please find my CV attached. > > Thank you & Best Regards, > > Muhammad Rehan Shaukat > Bioinformatician > Medical Research Council, Harwell > Mammalian Genetics Unit > Harwell Science and Innovation Campus > Oxfordshire > OX11 0RD > www.har.mrc.ac.uk <http://www.har.mrc.ac.uk/> > > On 8 March 2011 13:08, Peter Troshin <[email protected] > <mailto:[email protected]>> wrote: > > Hi Scooter, > > Great! Please feel free to update the proposal page accordingly! > > > http://biojava.org/wiki/Google_Summer_of_Code#Project_Proposals > > Regards, > Peter > > > > On 08/03/2011 11:44, Scooter Willis wrote: > > Peter > > Happy to co-mentor and make sure everything gets integrated > properly > into either core or another module. > > Thanks > > Scooter > > On Tue, Mar 8, 2011 at 6:15 AM, Peter > Troshin<[email protected] > <mailto:[email protected]>> wrote: > > Hi guys, > > Follow the invitation from Robert, I now registered this > idea on the GSoC > page for BioJava > > http://biojava.org/wiki/Google_Summer_of_Code#Project_Proposals > > I wonder if anyone of you fancy co-mentoring a student? > It would be good to have someone with up-to-date knowledge > of BioJava to > ensure that all the appropriate data structures are used. > My own knowledge > of BioJava is a bit rusty. > > Kind regards, > Peter > > > On 02/03/2011 05:12, Andreas Prlic wrote: > > Hi Peter, > > we still don;t know yet if we will have support from > Google again this > year. Once we have a confirmation we will use the wiki > site again for > hosting pages related to GSoC. However we should do > this project in > any case... > > Andreas > > On Mon, Feb 28, 2011 at 7:18 AM, Peter > Troshin<[email protected] > <mailto:[email protected]>> > wrote: > > What other functionality would you > like to see that is currently not there? > > I think that the methods below would be a good > starting point, then the > Google Summer of Code student can propose > something else that he/she > would > fancy implementing. > > Molecular weight > Extinction coefficient > Instability index > Aliphatic index > Grand Average of Hydropathy > Isoelectric point > Number of amino acids in the protein (His, Met, Cys) > > I know BioJava projects were managed under Open > Bioinformatics Foundation > (OBF) during last years GSoC. Is there a page for > this year GSoC ideas > somewhere? > > Regards, > Peter > > > On 25/02/2011 05:12, Andreas Prlic wrote: > > Great, seems we have an agreement that we want > to improve > functionality for this. How complex is this > going to be? From quickly > checking the 1.8 source it looks like just a > few classes that need to > be converted and not too painful. What other > functionality would you > like to see that is currently not there? > > Andreas > > > On Thu, Feb 24, 2011 at 8:08 PM, Scooter > Willis<[email protected] <mailto:[email protected]>> > wrote: > > We put in some basics regarding modeling > amino acid properties in the > core module but really didn't have any > pressing use cases to drive the > api beyond calculating the mass of a > peptide. We currently have > getMolecularWeight() as a method in > AbstractCompound but never added a > getSequenceMolecularWeight() to > AbstractSequence. It would be great to > get the attributes/features of amino acids > properly modeled in core > and extend when reasonable useful summary > methods at higher levels. > You should be able to query mass of a > peptide and have it valid for an > amino acid with a PTM which means the > amino acid needs to support the > ability to be modified in a flexible > manner. I spent the last year+ > developing a software suite for peptide > detection in MS data for > deuterium exchange where automated PTM > detection was important. Would > be great to get some focused attention on > the core to make sure we can > model nucleotides and amino acids with a > chemistry friendly API. > > Thanks > > Scooter > > On Thu, Feb 24, 2011 at 2:15 PM, George > Waldon<[email protected] > <mailto:[email protected]>> > wrote: > > Hello Peter& Andreas > > I effectively did some work on these > methods, mostly fixing and adding > the > ExPASy algorithm that was kindly > provided to me. I think it makes a > lot > of > sense to port all physico-chemical > property calculations related to > amino > acids and polypeptides to bj3, as > suggested by Andreas, and I > definitively > support the effort. We could smoothly > deprecate the bj1 package when > this is > done. Let me know how I could help. > > Thanks > George > > Quoting Peter > Troshin<[email protected] > <mailto:[email protected]>>: > > Hi Andreas, > > In fact I'd be happy to help with > the development of the tools for > simple > physico-chemical properties > calculation for peptides. We could > port > George’s > code (assuming he is happy with > this) from BioJava 1.8 but we can > also > provide a few other methods. A > couple of projects in the lab where I > work > would have benefited from having > these calculations readily > available. > > I was thinking about participation > in the Google Summer of Code > (GoSC) > this year as a mentor, and I think > this would be an easy project for > a > student. What do you think about this? > > Thank you for your prompt reply. > > Regards, > Peter > > > > On 24/02/2011 16:54, Andreas Prlic > wrote: > > Hi Peter, > > if you get a copy of biojava > 1.8, it is still there. > However I would > like to port this to biojava 3 > as well.. George do you want > to help > me > with that, since you are one > of the authors of this > package? The > basic > support for chemistry in > BioJava 3 is a bit better... > (e.g. Element > class) > > Andreas > > On Thu, Feb 24, 2011 at 7:33 > AM, Peter > Troshin<[email protected] > <mailto:[email protected]>> > wrote: > > Hi, > > I've noticed that BioJava > up to about version 1.7 had an > org.biojava.bio.proteomics > package, which had methods for > isoelectric > point > and molecular weight > calculations for peptides. > I could not find > this > package in the BioJava > 3.0.1 API. I’d like to use > these methods and > wonder > if there are any > equivalent methods > available in the latest > version > of > BioJava? > > Thank you for your help, > > Kind regards, > Peter > > Dr Peter Troshin > Bioinformatics Software > Developer > Phone: +44 (0)1382 388589 > Fax: +44 (0)1382 385764 > The Barton Group > College of Life Sciences > Medical Sciences Institute > University of Dundee > Dundee > DD1 5EH > UK > > > > _______________________________________________ > Biojava-l mailing list - > [email protected] > <mailto:[email protected]> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ > Biojava-l mailing list - > [email protected] > <mailto:[email protected]> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > <mailto:[email protected]> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l