[Biojava-l] Isoelectric point and molecular weight calculations with BioJava
Peter Troshin
p.v.troshin at dundee.ac.uk
Tue Mar 8 14:01:01 UTC 2011
Hi Udana,
I'd suggest looking at the BioJava 1.8 code for isoelectric point and
molecular weight calculations for peptides, as this is something you
would need to port to BioJava3. Study BioJava 3 API, in particular
examine the data structures for representing peptides. For more ideas
look at http://www.expasy.org/tools/ web site.
Hope that helps.
Good luck with your application!
Regards,
Peter
On 08/03/2011 13:42, udana chathuranga wrote:
> Hi Peter,
>
> I am a student from university of moratuwa reading for my engineering
> degree in Computer Science Engineering and I am planning to
> participate in this year GSoC.I went through your project idea and
> sound like it perfect idea for me as I have done a bioinformatics
> course for my degree.
>
> What are the areas that I have study apart from the one you have
> mention in the idea?.
>
> Regards
> Udana
>
> On Tue, Mar 8, 2011 at 6:38 PM, 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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