[BiO BB] Best Bioinformatics and Database Education

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Fri Oct 31 03:37:46 EST 2003


> Hi Group,
>
> As a C++, VB, .NET programer, also experienced in SQL
> I'm very interested to get into the bioinformatics
> either in programming or in database architecture,
> administration.
>
> What are the modules I should get used to (I've heard
> of Bioperl) ?
>
> Is a certification in Biology or similar mandatory?

This is an interesting question. I think the process of
data modeling is like domain modeling, so in this respect
I think a good understanding of the concepts underlying
the data is important. I.e. You need a certain amount of
domain knowledge.

Naturally this doesn't affect the techical aspects of data
normalization given a good data model, but often normalization
is a pain for end users, who have clear ideas about what
data is conceptually related, and don't want to have to
manually link such data over several tables.

However, if your end users are screened from the underlying
data it is no problem, but then I think you are in the field
of application developement. This may be associated with
bioinformatics, but isn't really any different from any other
kind of engineering work.

I think some really important developement would be to allow
individual (domain experts) to create individual domain models,
which could then be openly shared / linked etc.

Cheers,
Dan.


> Thank you
>
> Denis
>
> On Thu, 30 Oct 2003 12:01:33 -0500 (EST),
> bio_bulletin_board-request at bioinformatics.org wrote:
>
>>
>> When replying, PLEASE edit your Subject line so it is
>> more specific
>> than "Re: BiO_Bulletin_Board digest, Vol..."
>>
>>
>> Today's Topics:
>>
>>    1. Molecular Mechanics (Universal Force Fields
>> models) (Miguel Pignatelli)
>>
>> --__--__--
>>
>> Message: 1
>> From: "Miguel Pignatelli" <Pignatelli at noraybio.com>
>> To: <bio_bulletin_board at bioinformatics.org>
>> Date: Thu, 30 Oct 2003 10:43:03 +0100
>> Subject: [BiO BB] Molecular Mechanics (Universal Force
>> Fields models)
>> Reply-To: bio_bulletin_board at bioinformatics.org
>>
>> This is a multi-part message in MIME format.
>>
>> ------=_NextPart_000_0033_01C39ED2.984F9920
>> Content-Type: text/plain;
>> 	charset="iso-8859-1"
>> Content-Transfer-Encoding: quoted-printable
>>
>> Hi,
>>
>> I'm trying to make a program in C that calculates the
>> energy of a =
>> molecule from the coordinates X,Y,Z of its atoms. We
>> want to apply the =
>> Universal Force Fields (UFF) described by Rappe. Once
>> we have the total =
>> energy of the molecule (contribution from each
> chemical
>> bond (bond =
>> stretching), angle bending, torsional terms, improper
>> torsions, out of =
>> plane bending motions and non-bonded interactions
>> (electrostatic and Van =
>> der Waals forces)) we will look for energy
> minimisation
>> through the =
>> conjugate gradient minimisation method.
>>
>> I am looking for a similar software to look at or any
>> algorithm that =
>> could help me. First of all I would like to know what
>> is the best data =
>> structure to use in this kind of software and if there
>> is any similar =
>> software to look at its code or any algorithm that
>> implements the UFF.
>> =20
>> The software imput will be atoms and coordinates, so
> it
>> will determine =
>> which atoms are bonded. Is there any efficient
>> algorithm for that?
>> =20
>> Any suggestions?
>>
>> Thanks all
>>
>> ------=_NextPart_000_0033_01C39ED2.984F9920
>> Content-Type: text/html;
>> 	charset="iso-8859-1"
>> Content-Transfer-Encoding: quoted-printable
>>
>> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0
>> Transitional//EN">
>> <HTML><HEAD>
>> <META content=3D"text/html; charset=3Diso-8859-1" =
>> http-equiv=3DContent-Type>
>> <META content=3D"MSHTML 5.00.3809.1800"
>> name=3DGENERATOR>
>> <STYLE></STYLE>
>> </HEAD>
>> <BODY bgColor=3D#ffffff>
>> <DIV><FONT face=3DArial size=3D2>
>> <DIV><FONT face=3DArial size=3D2>Hi,</FONT></DIV>
>> <DIV>&nbsp;</DIV>
>> <DIV><FONT face=3DArial size=3D2>I'm trying to make a
>> program in C=20
>> that&nbsp;calculates the energy of a molecule from the
>> coordinates X,Y,Z =
>> of its=20
>> atoms. We want to apply the Universal Force Fields
>> (UFF) described by =
>> Rappe.=20
>> Once we have the total energy of the molecule
>> (contribution from each =
>> chemical=20
>> bond (bond stretching), angle bending, torsional
> terms,
>> improper=20
>> torsions,&nbsp;out of plane bending motions and
>> non-bonded interactions=20
>> (electrostatic and Van der Waals forces)) we will look
>> for energy =
>> minimisation=20
>> through the conjugate gradient minimisation
>> method.</FONT></DIV>
>> <DIV>&nbsp;</DIV>
>> <DIV><FONT face=3DArial size=3D2>I am looking for a
>> similar software to =
>> look at or=20
>> any algorithm that could help me. First of all I would
>> like to know what =
>> is the=20
>> best data structure to use in this kind of software
> and
>> if there is any =
>> similar=20
>> software to look at its code or any algorithm that
>> implements the=20
>> UFF.</FONT></DIV>
>> <DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
>> <DIV><FONT face=3DArial size=3D2>The software imput
>> will be atoms and =
>> coordinates,=20
>> so it will determine which atoms are bonded. Is there
>> any efficient =
>> algorithm=20
>> for that?</FONT></DIV>
>> <DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
>> <DIV><FONT face=3DArial size=3D2>Any
>> suggestions?</FONT></DIV>
>> <DIV>&nbsp;</DIV>
>> <DIV><FONT face=3DArial><FONT size=3D2>Thanks=20
>> all</FONT></FONT></DIV></FONT></DIV></BODY></HTML>
>>
>> ------=_NextPart_000_0033_01C39ED2.984F9920--
>>
>>
>>
>> --__--__--
>>
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