[BiO BB] Seeking Bioinformatics positions in UK

Jeremy Smith jezza_com at hotmail.com
Thu Mar 14 12:26:18 EST 2002

Looking for any relevant Bioinformatics positions in the UK,
especially in or near Cambridge.

I have programming skills in QT/Linux/C++/Perl/Java/PHP, and also
a MRes in Bioinformatics from the University of York, UK.


Please find a text version of my CV below.


Version current as of : 14.Mar.2002
Microsoft Word format CV available on request.


Name : Jeremy Smith.
Date of Birth : 13.02.78.
Address : York. Please E-mail me for contact details.
Telephone : Please E-mail me for contact details.
E-Mail : jezza_com at hotmail.com.
Nationality : British.


1999 - 2000 MRes Bioinformatics : University of York.
(Comprises three projects, and a set of modules,
please see later for description.)

1999 Summer Internship University of York.
Statistical analysis of microarray probe effectiveness
in yeast using C (Prof. Rod Hubbard).  Internship was
gained by my performance in the Bioinformatics
MRes interviews.

Skills gained: LINUX, vim, C, statistical analysis.

1996 - 1999 BSc in Biology (genetic module bias) at
University of York, 2.1 grade. Third year Bioinformatics
research project (1999) entitled : "A phylogenetic
study of SINE sequences in the Sus scrofa genome
using ClustalX and BLAST"

(Prof. John Sparrow, Prof. Young)- proposed new
relationships, and discovered a possible link with
T-RNAs, to which high homology was shown.

1994 - 1996 Sixth Form College, Colchester : 4 'A' levels -
Chemistry (B), Biology (C), Art and Design (A),
General Studies (C).

1990 - 1994 Philip Morant School, Colchester : 10 GCSEs
including Maths, English, Geography, Art and Design.


High level Bioinformatics programmer/manager.

I have began programming at the age of 6, and have a genuine
fascination with Bioinformatics.


2000 Perl/Java Developer for Yacc Labs, Leeds. Dynamically
generated web sites using Perl CGI/DBI, liasing with
customers to establish their needs.

2001 - 2002 Perl/Java Developer for PA News
(the Press Association), Howden.  Database management
with Perl DBI, XML generation/DTD design, XSLT processing.
Produced a Perl script which generated valid XML from
a database transaction.

MRes Bioinformatics Course Overview October 2000

Fall Term :
(	Introduction to Computers.	(	Molecular Sequence Analysis.
(	Genomics.			(	Neural Nets.
(	Numerical Skills I.		(	Skills in Presentation.
(	Introduction to Programming (Java).

Spring Term :
(	Molecular Structure. 		(	Structural Bioinformatics (Quanta).
(	Logic and Learning.		(	Molecular Aspects of Disease (essay).
(	Numerical Skills II. 		(	Transferable Skills I.
(	Perl Programming.

Student Project I - "Three dimensional visualisation of
conserved active site residues within catalase." -
Poster presentation.

Student Project II - "Salmon stock separation using
Kohonen Neural Network techniques".

Description :

A large data-set of salmon scale micro-photographs was
made available from a PhD thesis.   These had been
classified by river locality and the aim of the project
was to somehow train a neural network to classify an
unknown scale upon presentation.

The Kohonen neural network provides topographical
clustering of classes - visually separating the inputs.
Annuli are yearly bands which can be used to determine
the age and locality of a specimen, an algorithm to
detect and highlight annuli was devised.

A data set of annuli was used to train the Kohonen neural
network - and known scales were presented.  The network
could separate scales from two of the rivers (classes),
but not the third.

Student Project III (3 months) at UCL, London. :

Project Title:

"An online microarray database with data submission and
retrieval facilities, extended with the addition of
online clustering of user submitted data"

Abstract from the project :

   "The sheer pace of oligo-nucleotide microarray data
generation has dictated new demands on computer hardware,
not just in terms of processing and analysis, but also storage
and accessibility.  The diverse medium of the Internet
offers new prospects for centralised data repositories,
online clustering of expression data, and information
dissemination of academic progress in microarray

   This project offers an Internet-based microarray
resource consisting of a MySQL database  with submission
and retrieval facilities, extended with an online
analysis facility offering all the functionality of
Gavin Sherlock's XCluster (a UNIX command line
microarray clustering program).  It is the only
Internet facility currently which offers the important
SOM and K-means clustering methods."

This project was awarded 72%.  PDF available on request.

Supervisor quote:

"Jeremy has created a micro-array database that will
not only be a valuable resource for our own data
management and analysis, but will provide access for
the general community and a convenient and accessible
format.  Jeremy's efforts may well influence the
further development of micro-array databases, and
he achieved these results with very little input and
guidance.  A very good performance" - Professor D.
Goldstein Supervisor, UCL.


Talented Object Oriented Programmer

Fluent - QT3 on Linux/GCC 2.96 application
development.  A recent 3 month project in my spare
time has been the design and realisation of a
Kohonen neural network in C++.  Understand makefiles,
const, header files, inheritance and polymorphism,
pointers, references, debugging. C++ is my favourite
language and Linux my favourite development environment.

Fluent - including experience with LDP, Telnet, DBI,
CGI modules, use of taint mode and strict pragma.
Object-Oriented (OO) Perl used at all times,
(utilise my own modules/classes), and references.
Competent with regular expressions.  In a recent
Perl test at an interview, I came top out of all

Linux evangelist/geek - Linux is my favourite personal
hobby, and work environment.  Member of the local Linux
User Group at York.

Linux skills :

.  Kernel re-compilation, can update a distro with a
newer kernel, load modules etc.

.  Configuration of various services, Apache, MySQL,
adding/removing RPMS, compiling tarballs.
Understanding library dependencies, troubleshooting.

Competent level - Two month's Java course/training
and assessment on Masters of Research course.
Fully understand OOP/Swing/Java2d/Swing etc.

SQL - Competent level - database design, implementation
construction of SQL queries.  Commercial experience
with Informix and MySQL databases - used MySQL for
my microarray database.

XML - Experienced level - can write XML, DTDs,
validation and transformation using XSLT stylesheets
(to HTML).

C-Sharp (C#) (.NET) - Average Level - Implemented
Kohonen neural network in C-Sharp (Microsoft's
answer to Java)- much faster processing and GUI
than Java equivalent.

PHP4 - Average level - very similar to Perl, except
embedded in HTML.

Windows 2000 - First relatively stable Microsoft OS,
basic admin and configuration, platform for .NET.

PC Building - Built several PCs in the past,
including my own current machine.


Microarray clustering and statistical analysis

Partitioning methods : SOM, K-means and hierarchical
clustering.  I have implemented a Kohonen neural
network in C++ in my spare time.

Distance methods : Euclidean distance, Pearson


Any suitable Bioinformatics position, although
preferably within Cambridge, UK or within distance.


Avid Thai kick boxer.
Like to play Badminton.
Full clean driving licence.


Tim Hartley
PA News,
E-mail: tim.hartley at pa.press.net

Chat with friends online, try MSN Messenger: http://messenger.msn.com

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