Re: Isoelectric point and molecular weight calculations with BioJava

Hi Andreas,

It's not a lot to wait before we know whether Google supports OBF this 
year or not.
According to the GSoC timeline 
(http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs#timeline 
) on the 18 of March they will publish the list of organisations they 
will support. Let's wait and see.

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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>>>>>>>>
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>>
>
>

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