Hi Peter,
On Tue, Mar 8, 2011 at 6:38 PM, Peter Troshin <[email protected]>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<[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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
