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

Tue Mar 8 11:44:59 UTC 2011

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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