Re: Isoelectric point and molecular weight calculations with BioJava

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]>  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]>
>>>   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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