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

Tue Mar 8 13:42:32 UTC 2011

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>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>
>>  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
>>>> >
>>>>  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>
>>>>>>  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>
>>>>>>>  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>:
>>>>>>>>
>>>>>>>>  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>
>>>>>>>>>>  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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>>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>
>>>
>>>
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