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Hi Omer, <br>
<br>
Please find below my point by point answers to your questions. <br>
<br>
Point 1:<br>
You need to show how to calculate the value i.e. give the formula
with necessary explanations. <br>
For example:<br>
Molecular weight of a peptide is a sum of molecular weights of its
compenents. <br>
<br>
<div align="center"><img
src="cid:part1.04050107.07060909@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>
<br>
Point 2:<br>
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<![endif]-->I do not think that the idea that you describe is well
linked with the overall aims of the project. I was thinking about
adding some
other physico-chemical property calculation for the peptide, protein
or nucleic
acid.<span style=""> </span>
<br>
<br>
Point 3:<br>
I am not sure there is one. I'd suggest explaining a little bit more
what you mean by "BioJava time table" and posting this question to
the BioJava mailing list. Someone else may point you in the right
direction. <br>
<br>
I hope that answered your questions. <br>
<br>
Regards, <br>
Peter<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
You do not need to provide any implementation details for it. <br>
<br>
On 05/04/2011 20:33, omer f wrote:
<blockquote
cite="mid:BANLkTinfMi-XDkqnnxrVnMqfjaLttHuEKQ@mail.gmail.com"
type="cite">
<div dir="ltr">Dear Peter,<br>
<br>
Thank you for your detailed answer :)<br>
<br>
Today and Yesterday i have started to read the relevant
background material About the subject,<br>
I will be sincere, I can't say i really understood all the
specific Biological Data evolve it, I related more to
the Chemistry and Calculations. Even though, i think i could
handle and learn all needed for the completion of this project. <br>
<br>
<div>I have three questions that relates to the project:<br>
1. In my proposal and application on what subjects i need to
specify and focus: The actual way i am going to Calculate and
program each function, or i should Show and Explain the way i
am going to execute and plan the time table for the project?<br>
2. While doing the example exercise I got a new Idea that
could be part of this project, or can be a new project (or
maybe it already implemented):<br>
I thought about Creating a "Sequence Manager" which will be
based on Server-Client program. </div>
<div>The "Sequence Manager" (as i call it) the Server will Get
commands for calculations needed to be execute. The Server
will connect </div>
<div>his "Clients" (other computer) and sending them
the relevant Files (input\output) and Calculation commands
need to be execute. (like the "Amino Acid" project
functions). After clients finish the process and calculation,
they connect the server and sends him the relevant files
(output) and ready for furthermore calculations. I this kind
of implementation will help to Speed up process, and with the
right features like Priority Queue That will Define to Server
which Commands more important to calculate etc. </div>
<div>I Hope this idea isn't implemented yet (:)) and if so, Do
you think it a good Idea or kind of ideas to Suggest?? </div>
<div>3. The Last question for today, about Administration: Where
could i find the BioJava Time table for the project??</div>
<div><br>
</div>
<div>Sincerely, </div>
<div>Omer. </div>
<div><br>
</div>
<div><br>
</div>
<div>meaning the Sequence Manager (server) will Get Commands for
calculation on specific Files (input and output) and will send
it to other clients to calculate them using the
<div>
"Amino acic Calculator" which the original project develops.
the purpose of using this program is to calculate thing
faster in more than</div>
<div>on client (computer). <br>
<div><br>
<div class="gmail_quote">2011/4/4 Peter Troshin <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:p.v.troshin@dundee.ac.uk"
target="_blank">p.v.troshin@dundee.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi Omer,<br>
<br>
I am on the BioJava list so I got your email.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
>> I am in the second year of my degree, and
so far i have learned<br>
>> the program languages: Java, C, C++ and
in addition Object<br>
>> Oriented Programming in Java.<br>
</blockquote>
<br>
</div>
Sounds good!
<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
>> Though, i have no working experience in
programming.<br>
</blockquote>
<br>
</div>
Thank you for being honest (:-))
<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
>> My only concern is, will My lack of
experience could hurt my<br>
>> chances to be accepted to the project.<br>
</blockquote>
<br>
</div>
It may but it may not. Some people pick up things
pretty quickly - are you one of them?<br>
Seriously, have a look at the methods that you are
about to implement, search the web<br>
for more information about them and see if you have a
good idea how to do that. You do not have to know
anything about the BioJava at this stage, you can
learn about it later. For this<br>
project you also need to know the basics of Chemistry
and Molecular Biology, nothing too<br>
complicated, but still without this knowledge the
learning curve for this project is going to be pretty
steep.<br>
<br>
I hope I answered your question.<br>
<br>
Regards,<br>
Peter
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<br>
<br>
<br>
On 04/04/2011 13:59, omer f wrote:<br>
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To all it may concern,<br>
<br>
Dear BioJava,<br>
<br>
My name Omer Frieman and i am a student of
Computer Science (B.Sc)<br>
and International Politics at the Hebrew
university in Jerusalem,<br>
Israel. Last week, I attended a conference
about Google SOC, Which i<br>
find most interesting and something that i
would like to experience.<br>
I am in the second year of my degree, and so
far i have learned the<br>
program languages: Java, C, C++ and in addition
Object Oriented<br>
Programming in Java. Though, i have no working
experience in<br>
programming.<br>
<br>
While searching the list of SOC projects i came
across the<br>
Bioinformatics Foundation Projects. I found the
Java Project very<br>
interesting, First, for the content - the
research subject of<br>
Bio-informatics, and Second, I was looking
specifically for a Java<br>
project for gaining experience in it,<br>
<br>
Before sending my application with the short
coding exercise, i send<br>
you this mail to Introduce myself. My only
concern is, will My lack<br>
of experience could hurt my chances to be
accepted to the project. I<br>
would appreciate your opinion in that matter.<br>
<br>
Furthermore, i was wondering how do i connect
the Project mentor<br>
(Peter Troshin).<br>
<br>
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Sincerely, Omer.
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