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1 | | -'''Amino Acids Physico-Chemical Properties Calculation''' |
| 1 | +'''Amino Acids Physicochemical Properties Calculation''' |
2 | 2 |
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3 | 3 | ''[[Google Summer of Code]] Project by [[Chuan Hock Koh]]'' |
4 | 4 |
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5 | 5 | ''Mentored by [http://biojava.org/wiki/User:Ptroshin Peter Troshin]'' |
6 | 6 |
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7 | 7 | ''Co-mentored by [[Andreas Prlic]]'' |
8 | 8 |
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9 | | -The calculation of physico-chemical properties for biopolymers is an important tool in the arsenal of molecular biologist. Theoretically calculated quantities like extinction coefficients, isoelectric points, hydrophobicities and instability indices are useful guides as to how a molecule behaves in an experiment. Many tools for calculating these properties exist, including widely used open-source implementations in EMBOSS and BioPerl, but only some are currently available in BioJava3. The aim of this project is to port or produce new implementations of standard algorithms for a range of calculations within BioJava3 and make them available in various levels (APIs, executable and web service). |
| 9 | +The calculation of physicochemical properties for biopolymers is an important tool in the arsenal of molecular biologist. Theoretically calculated quantities like extinction coefficients, isoelectric points, hydrophobicities and instability indices are useful guides as to how a molecule behaves in an experiment. Many tools for calculating these properties exist, including widely used open-source implementations in EMBOSS and BioPerl, but only some are currently available in BioJava3. The aim of this project is to port or produce new implementations of standard algorithms for a range of calculations within BioJava3 and make them available in various levels (APIs, executable and web service). |
10 | 10 |
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11 | 11 | ==Properties== |
12 | 12 | Listing the properties that could be considered for implementing. Mainly based on the original proposal, PROFEAT and Sirius PSB. |
@@ -117,8 +117,8 @@ Likewise, Sirius PSB transforms sequences accordingly to their respective groupi |
117 | 117 | * Created a user page for myself on BioJava Wiki. |
118 | 118 | * Introduced to the biojava developer mailing list. |
119 | 119 | * Request for input and suggestion from biojava developer mailing list on this project. |
120 | | -* Committed the first draft of the interface class for the basic physico-chemical properties. |
121 | | -* Updated interface class for basic physico-chemical properties based on Mentors' feedback. |
| 120 | +* Committed the first draft of the interface class for the basic physicochemical properties. |
| 121 | +* Updated interface class for basic physicochemical properties based on Mentors' feedback. |
122 | 122 | * Learned and better understand how to use Maven on Eclipse. |
123 | 123 |
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124 | 124 | ===May 13 - May 20 (Week 3)=== |
@@ -274,9 +274,9 @@ Likewise, Sirius PSB transforms sequences accordingly to their respective groupi |
274 | 274 | * Completed the integration of AAProperties.jar with JABAWS |
275 | 275 | * Checked all links on http://biojava.org/wiki/GSoC:AAPropertiesComputation |
276 | 276 | * Rectified two links http://web.expasy.org/protparam/ and http://web.expasy.org/compute_pi/ |
277 | | -* Checked all links on http://biojava.org/wiki/BioJava:CookBook under Physico-Chemical Properties Computation |
| 277 | +* Checked all links on http://biojava.org/wiki/BioJava:CookBook under Physicochemical Properties Computation |
278 | 278 | * Linked up the executable jar file on maven to Cookbook |
279 | | -* Simplified the section under Physico-Chemical Properties Computation on http://biojava.org/wiki/BioJava:CookBook |
| 279 | +* Simplified the section under Physicochemical Properties Computation on http://biojava.org/wiki/BioJava:CookBook |
280 | 280 | * Added dummy id to be allowed in the xml file of AminoAcidComposition. |
281 | 281 | ** It will be used in future as an option to compute the mass of amino acid instead of based only on elements. |
282 | 282 |
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