[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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