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Hi Krzysztof, <br>
<br>
I think you can strengthen your proposal if you can demonstrate that
you understand how to calculate the physico-chemical properties
mentioned in your proposal. <br>
<br>
For example:<br>
Molecular weight of a peptide is a sum of molecular weights of its
components. <br>
<br>
<div align="center"><img
src="cid:part1.02070904.02080907@dundee.ac.uk" alt="The equation
for the molecular weight of a peptide."></div>
<p style="line-height: 16px;">where <i>N<sub>i</sub></i> are the
number, and <i>M<sub>i</sub></i> the average <i>residue</i>
molecular weights, of the amino acids. <i>M<sub>N</sub></i> + <i>M<sub>C</sub></i>
are added to the total in order to account for the termini: H at
the N-terminus and OH at the C-terminus. Of course, if the termini
are modified, these additions are replaced by those of the
modifiers.<br>
Average <i>residue</i> molecular weights of the amino acids (<i><sub>Mi</sub></i>)
can be found in the reference tables <URL>.<br>
</p>
<p style="line-height: 16px;">As for your other questions: <br>
</p>
<p style="line-height: 16px;">1) Do you mind adding some tests to
short-coding-exercise? :)
<br>
</p>
<p style="line-height: 16px;">I'll let you decide on that. I'd
suggest doing it in a way the Java programmer would. <br>
</p>
<p style="line-height: 16px;">2) Should I mention
short-coding-exercise at all in proposal? </p>
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</p>
<p style="line-height: 12pt;">It would not hurt to mention it. It
will be my
task to ensure that all the mentors have access to your coding
exercise. I do
not know yet how to link your proposal with the short coding
exercise. Somehow
I will have to figure this out. </p>
<p style="line-height: 16px;"> </p>
I hope that helps. <br>
<br>
Regards, <br>
Peter<br>
<br>
<br>
<br>
On 06/04/2011 20:15, Krzysztof Ropiak wrote:
<blockquote cite="mid:4D9CBBC8.80403@gmail.com" type="cite">Hi,
<br>
It time for my proposal draft. I hope I've included all my
thoughts about project.
<br>
And few more questions:
<br>
1) Do you mind adding some tests to short-coding-exercise? :)
<br>
2) Should I mention short-coding-exercise at all in proposal?
<br>
<br>
Proposal:
<br>
<br>
Project name :
<br>
Amino acids physico-chemical properties calculation
<br>
<br>
Student:
<br>
Krzysztof Ropiak (+contact information here)
<br>
<br>
Abstract:
<br>
<br>
The basic aim of this project is to develop new high-performance
implementations of standard algorithms for a range of calculations
within BioJava3.
<br>
Calculation examples:
<br>
1. Molecular weight
<br>
2. Extinction coefficient
<br>
3. Instability index
<br>
4. Aliphatic index
<br>
5. Grand Average of Hydropathy
<br>
6. Isoelectric point
<br>
7. Number of amino acids in the protein (His, Met, Cys)
<br>
<br>
<br>
About me:
<br>
<br>
I am second year student at Gdansk University of Technology
(Poland). If accepted, it would be my first time to work in an
open source project - however I really like OS idea and I'm hoping
for first experiences in that regard. I am Java technology
enthusiast and high-quality code fan. Another thing is that I feel
really comfortable with algorithms. I have participated in number
of algorithmic contests - as an example, I have achieved Second
Round of last year's Google Code Jam (-- is link needed here? :)
--). I've got also knowledge about multithreaded processing. I
know more that few design patterns and I'm ready to recognize
situations where they are needed. I am familiar with modern Java
frameworks - ex. Sprint, Hibernate - I've read that BJ3 should be
easy to work with them. Each day, I am doing my best to write
clean code.
<br>
<br>
Weak points:
<br>
<br>
I can see two of them:
<br>
- Time of my participating in GSOC would be limited in first two
weeks as academic year in Poland is not yet finished. Fortunately,
I am not kind of student, who has problems with studying and I am
sure I can work before my studies finishes. I will not be able to
work in the last week of GSOC, because of travelling.
<br>
- I am computer science student, not biology (and others). My
knowledge is not really big here. Still, I strongly believe I can
contribute without it.
<br>
<br>
<br>
Project basic plan:
<br>
<br>
Before GSOC start:
<br>
Getting in touch with BioJava
<br>
Looking for all knowledge needed to calculate properties
mentioned above
<br>
Looking for best (usually faster) methods to calculate
properties.
<br>
<br>
Coding part :
<br>
<br>
May 24 - June 10
<br>
Molecular weight
<br>
June 11 - June 20
<br>
Extinction coefficient
<br>
June 20 - June 30
<br>
Instability index
<br>
July 1 - July 10
<br>
Aliphatic index
<br>
July 11 - July 20
<br>
Grand Average of Hydropathy
<br>
July 21 - July 31
<br>
Isoelectric point
<br>
August 1 - August 10
<br>
Number of amino acids in the protein (His, Met, Cys)
<br>
<br>
August 11 - till the end of GSOC:
<br>
Finishing documentation & all other things to polish whole
work done and make it as much valuable for BJ as possible
<br>
<br>
<br>
** This is just a basic plan. Order of calculations can be changed
due to mentor's ideas. In this plan I reserved more that two weeks
for first calculation, due to my limited time at start. All other
calculations are supposed basically to implemented up to 10 days.
I think there is a possibility of me doing more that just these
calculations and I strongly hope I can finish these calculations
much quicker that planned and spend some time on polishing work
done previously or some other mentor's ideas.
<br>
<br>
** I would like to use test-driven-development approach, which
would make sure code is tested properly. Implementing particular
calculations would be finished with providing javadoc and other
documentation.
<br>
<br>
Hope you enjoyed reading :)
<br>
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Krzysztof Ropiak
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