Re: Biohackathon in Cape Town
Quoting Paul Makepeace ([EMAIL PROTECTED]): > Open Source software folk try to get their selves aligned in a freeform > bioinformatics hackfest in SA. O'Reilly implicated as organisers. > > http://www.businessday.co.za/bday/content/direct/1,3523,1032294-6099-0,00.html > Up to date news can be found on http://www.technophage.com/ Kris, -- Kris Boulez Tel: +32-9-241.11.00 AlgoNomics NV Fax: +32-9-241.11.02 Technologiepark 4 email: [EMAIL PROTECTED] B 9052 Zwijnaarde http://www.algonomics.com/
(forw) Ensembl job openings
Might be intresting for some of you. Kris, - Forwarded message from Ewan Birney <[EMAIL PROTECTED]> - Date: Wed, 10 Jul 2002 11:25:18 +0100 (BST) From: Ewan Birney <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Subject: Ensembl job openings We have opened some new jobs on the EBI side of the Ensembl project due to additional funding (although two of the jobs - the web position and the GRID researcher are in fact project managed by Sanger people). Ensembl is an exciting, world leading bioinformatics group on the Hinxton campus, focused on Genome informatics. You can apply directly at http://www.embl.de/ExternalInfo/jobs/ For people who would like to informally get in contact about the job positions, please email myself ([EMAIL PROTECTED]) directly. I would appreciate it if people could pass this mini-advert on to anyone in their wider group who might be interested - we are looking for enthusiastic, interested people in genome informatics. --- Position: Mosquito Genome Web developer Ensembl (http://www.ensembl.org/) is a world-leading bioinformatics project for generating and viewing automatically annotated public genome data. We are looking for enthusiastic web developers to help build and manage our rapidly expanding range of Ensembl web services. The role will involve all aspects of site design and development from the back-end database systems through to the design and implementation of web interfaces. You should possess excellent teamwork and communication skills, enjoy technical challenges and have an eye for detail. You must have experience in web interface design, and ideally will have a degree-level background in biological science. Experience with Perl, SQL, UNIX and XML will be advantageous, as would an understanding of mosquito biology. As part of your application, you should submit a URL for a website you have designed/programmed. -- Position: Data orientated genome informatician We are looking for an enthusiastic researcher for genome data manipulation and development. Working in the world leading Ensembl group for genome informatics, the successful candidate will be examining, integrating and developing new data sources and technologies. The successful candiate will have either a masters or PhD in either molecular biology or computer science and have experience with database technologies, such as SQL. UNIX background and programming ability are beneficial. Molecular biologists with self taught IT skills are encouraged to apply only if they can show at least 2 years experience with UNIX systems including some programming skills. - Position: Molecular Biology ontologist/curator We are looking to expand our molecular biology knowledgebase program and are looking for enthusiastic researchers in this area. The successful candidate could either be a molecular biologist at PhD level with confident computing skills, or an computer science masters level or higher with AI and ontology experience. In the case of a molecular biologist, you must have at least 2 years experience with UNIX and at least some programming skills. For Computer scientists, previous bioinformatics experience is very useful and, lacking that, demonstrable interest in biological sciences. -- Position: Biological GRID researcher We are looking for an enthusiastic researcher for a large scale, multi-site computing project. The successful candidate should have exposure to large scale HPTC and a background in biology, a physical science or IT. Successful candidates will have either a masters or PhD within their scientific discipline or lengthy experience of large scale system administration (ca. 500 nodes). System administration skills, ideally with Tru64 and Linux are also required. Experience with multiple forms of distributed resource management, Perl and SQL are all beneficial. - End forwarded message -
Writing XML from Perl
What is peoples preferred module for writing XML (files) from within Perl ? The data is read by a perl script from different (heterogeneous) sources and stored internally in a tree of objects. I looked around a bit and saw XML::Writer being mentioned a lot. Is it this what most people are using ? Kris, -- Kris Boulez Tel: +32-9-241.11.00 AlgoNomics NV Fax: +32-9-241.11.02 Technologiepark 4 email: [EMAIL PROTECTED] B 9052 Zwijnaarde http://www.algonomics.com/
Re: Writing XML from Perl
Quoting Dominic Mitchell ([EMAIL PROTECTED]): [ ... ] Hereby I want to thank everyone for their suggestions. I'll have a look at the different options and make an educated choice. > > The important point is to not use print statements, because you'll get > it wrong. :-) > I did this for a project a few years ago and this was o so true :) Kris, -- Kris Boulez Tel: +32-9-241.11.00 AlgoNomics NV Fax: +32-9-241.11.02 Technologiepark 4 email: [EMAIL PROTECTED] B 9052 Zwijnaarde http://www.algonomics.com/
Parsing PHP code from Perl
I had a quick look around the net and couldn't find an answer, so I'll ask here. I'm looking for a way to parse (read in) a PHP file and gave the PHP variables available as Perl variables. Given an existing PHP application that get it's configuration by "include" ing a 'config.php3' file. I now want to use this config file from a perl script. Is there an easy way to get all the variables/defines/.. out of the PHP config file. I can of course write a little parser for this. Kris, -- Kris Boulez Tel: +32-9-241.11.00 AlgoNomics NV Fax: +32-9-241.11.02 Technologiepark 4 email: [EMAIL PROTECTED] B 9052 Zwijnaarde http://www.algonomics.com/
Re: Parsing PHP code from Perl
Quoting Leon Brocard ([EMAIL PROTECTED]): > Kris Boulez sent the following bits through the ether: > > > I'm looking for a way to parse (read in) a PHP file and gave the PHP > > variables available as Perl variables. > > If you could post an example couple of lines from the config file then > it'd be easier to tell you how to go about it. > [ I will respond here, thanks to all the other people that replied ] As there seems to be no straight forward solution (writing everything out via web page and parsing this with LWP sounds pretty convoluted), I'll just parse the php file myself. The config file will only be edited by me and the part I'm intrested in contains only simple variable and constant definitions. Shouldn't be too hard. Thanks
Re: [OT] Magazines
Quoting Dave Cross ([EMAIL PROTECTED]): > > > Sucks, I know, but then that's what you get for living in a world > where 95% of the inhabitants are stupid. > I have the impression it's more like 99% these days :( Kris,
Re: Learning regular expressions
Quoting Mark Fowler ([EMAIL PROTECTED]): > On Mon, 17 Mar 2003, Phil Dobbin wrote: > > > You can't go wrong with Jeffrey Friedl's `Mastering Regular Expressions' > > (O'Reilly: 1-56592-257-3). > > You'd be better off with the 2nd Edition. > > O'Reilly: 0-596-00289-0 > http://www.oreilly.com/catalog/regex2/ > > Shouldn't someone be reviewing this for the site? > I just finished reading it (privately). I agree that if you're serious about regexes, you should read this book. The second edition also contains chapters on Java, VB.net, .. Perl is still the main languange of this book though. After reading this book I was able to speed up a regex we're using in production by a factor of 4. Kris,
Re: Telewest + Linux + MAC(?) oddness
Quoting Andy Wardley ([EMAIL PROTECTED]): > Paul Makepeace wrote: > > I'm wondering if the modem is rejected the MAC of the linux box while > > the Windows's box's lease is still in effect or something bizarre like > > that. > > Yes. Or the DHCP server at the ISP. > > With NTL I had to switch off the cable modem for a few hours until the > DHCP lease expired. Then all was good. > [ this if for Telenet, a Belgian cable modem ISP ] With Telenet I even noticed that I can't get an IP adress for the same MAC addres when booting linux (dual boot). - boot machine windows 2000: gets IP address via DHCP - reboot machine to Linux : DHCP does not give IP address - reboot machine to Windows: gets IP address Waiting the DHCP expiry time solves the problem (as did adding a FW/router machine :) ). Kris,
Re: keyboards
Quoting David Cantrell ([EMAIL PROTECTED]): > On Wed, Oct 24, 2001 at 09:30:13AM -0400, Mz anathema wrote: > > Can anyone suggest a good way to recover a soup-soaked keyboard? > > > Alternatively, just buy a new keyboard. > Given the low cost of a decent keyboard ( ~1000 BEF, 25 euro) I'd suggest bying a new one. Kris, -- Kris Boulez Tel: +32-9-241.11.00 AlgoNomics NV Fax: +32-9-241.11.02 Technologiepark 4 email: [EMAIL PROTECTED] B 9052 Zwijnaarde http://www.algonomics.com/
