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 >>>> >> >> > > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
