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
<[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
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