[Biojava-l] Isoelectric point and molecular weight calculations with BioJava

Peter Troshin p.v.troshin at dundee.ac.uk
Tue Mar 8 14:21:18 UTC 2011


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 <p.v.troshin at dundee.ac.uk 
> <mailto:p.v.troshin at dundee.ac.uk>> 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<p.v.troshin at dundee.ac.uk
>         <mailto:p.v.troshin at dundee.ac.uk>>  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<p.v.troshin at dundee.ac.uk
>                 <mailto:p.v.troshin at dundee.ac.uk>>
>                  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<willishf at ufl.edu <mailto:willishf at ufl.edu>>
>                          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<gwaldon at geneinfinity.org
>                             <mailto:gwaldon at geneinfinity.org>>
>                              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<p.v.troshin at dundee.ac.uk
>                                 <mailto:p.v.troshin at dundee.ac.uk>>:
>
>                                     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<p.v.troshin at dundee.ac.uk
>                                         <mailto:p.v.troshin at dundee.ac.uk>>
>                                          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
>
>
>
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