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 >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Biojava-l mailing list - [email protected] >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Biojava-l mailing list - [email protected] >>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>>>> >>>> >>> >> >> > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
