[BiO BB] Seeking Bioinformatics positions in UK
return3 at forscience.com
Fri Mar 15 06:11:49 EST 2002
Dear Mr. Smith,
Thank you for your mail but unfortunately we are not based in the U.K. Thank
you all the same and wish you the best.
Dr. A. Gupta
----- Original Message -----
From: Jeremy Smith <jezza_com at hotmail.com>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Thursday, March 14, 2002 10:56 PM
Subject: [BiO BB] Seeking Bioinformatics positions in UK
> 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.
> CURRICULUM VITAE
> Version current as of : 14.Mar.2002
> Microsoft Word format CV available on request.
> PERSONAL DETAILS
> 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.
> CAREER OBJECTIVE
> High level Bioinformatics programmer/manager.
> I have began programming at the age of 6, and have a genuine
> fascination with Bioinformatics.
> COMMERCIAL EXPERIENCE (1 YEAR IN TOTAL)
> 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.
> RELEVANT SKILLS
> 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.
> RELEVANT INTERESTS
> 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
> POSITION SOUGHT
> Any suitable Bioinformatics position, although
> preferably within Cambridge, UK or within distance.
> OTHER SKILLS
> 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
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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