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]> 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]> 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]>
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]>:
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]>
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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