October 05, 2009
Self-imposed chaos in a time of crisis
So I'm quitting my job in Paris and moving to northern California. This would be a carefully planned move for some people, thought out and discussed with friends and family over many months. Me? I just said "fuck it", and bought the tickets. This is as a result of the less-than-fairytale outcome of the love affair that brought me to the City of Light. Maybe it's disproportionate (people fall in and out of love all the time without generally feeling the need to leave the country, right?) but my reason for being in Paris is not here any more, and, with such thin threads binding me to my situation, when they were cut, I was adrift. Avid readers of this blog, I am sure, will be aware of the mental turmoil I was in at the beginning of the year, and the hopes I had for improvement, and how that was quickly dashed. I thought that the latter part of the year would be different. I had hoped to find stability, built on the foundation of a life with the woman I loved. Because of her, I came to Paris. Because I came to Paris, I got a job.
So when she ended it, I could feel the darkness closing in again. What I am left with after our relationship is a friendship with her, which is what we were before we were together. But it will never be the same friendship. When someone lets you down like that, with such an apparent coldness, and lack of concern and empathy and understanding, when they disappoint you so badly, it is impossible to feel the same openness towards them afterwards. I would, at one point, have trusted her with my life - and in one sense, I did. But not now. So it has taken a couple of months for my life to return to an approximation of normality, and even now I am not entirely sure what's really normal.
The problem is that I came to Paris for her. If I had been here already and had made a life here, I would probably not be leaving. But I am living in our ex-shared apartment, and it seems strange to me to feel that I have now actually spent more time there on my own than together with her. Her presence still haunts me in the apartment. There, and in Paris itself - the places we ate at together, the walks we took in Parc Monceau, the museums we visited. So, to exorcise the ghost, I have to leave Paris.
Which means leaving the apartment and the job, of course. The irony is that I'm starting to enjoy Paris. I found a good writers' group, and one or two nice pubs. And of course the food and wine and culture is wonderful. But I am looking forward to seeing my family, and spending more than just a few weeks with them.
I do wonder what the next three months will bring. 2007 was unsettled, 2008 was strange, and this year has been like living in a Hieronymous Bosch painting sometimes. I am tired of the weirdness. I crave ... not routine, exactly, but I want control back over my life again.
So I choose to leave Paris. I will be living with my father and stepmother, who I know will not do anything weird to me and will let me live my life unimpeded.
What worries me now is the question of trust. I would like to meet someone, eventually, that I can settle down with. But right now, it seems like so much effort, and the question of whether I can trust someone not to hurt me again is one I can't answer right now. I never, ever expected Elise to do what she did. I guess I didn't know her as well as I thought I did.
Am I willing to take that risk ever again?
Posted by daen at 10:57 AM | Comments (0)
April 26, 2006
How to determine and recover from Winsock2 corruption
http://support.microsoft.com/kb/811259
Posted by daen at 08:20 PM | Comments (0)
February 18, 2006
Elsevier MDL 2006 European and UK Users' Group Meeting, London March 5-8
I'll be in London at the Park Hotel between March 5th and 8th for the Elsevier MDL 2006 European and UK Users' Group Meeting. I'm due to give a talk on Monday 6th on using MDL Cheshire for combinatorial enumeration of chemical compounds.
Cheshire is a chemical scripting language and an interactive prototyping environment for building, validating, and using "rules" that analyze and interpret chemistry. In other words, chemistry in a computer. Combinatorial enumeration is taking two or more groups of molecular fragments and joining them together in all the different possible combinations.
Easy, eh?
Posted by daen at 04:47 AM
August 12, 2005
Job hunting for the over 50's in Marin County
Marin County's Pacific Sun newspaper (Marin's Best Every Week) considers job hunting when you're over 50. I didn't realize that the Bay Area lost 400,000 jobs between 2001 and 2004. I nearly, nearly moved to San Francisco in 2001. Probably a good job I didn't. Anyway, you're probably wondering what the Pacific Sun could have to do with everyday life in Denmark ... Good question. Here's a photo of a young man presumably about to call time on an interview with some old timer.
Posted by daen at 02:28 AM
August 08, 2005
Genizon bought Global Genomics AB
A bit late (May 11, 2005) but still ...
GENIZON BIOSCIENCES ACQUIRES ASSETS FROM GLOBAL GENOMICS
TO ACCELERATE THE DISCOVERY OF DISEASE-CAUSING MUTATIONS AND TARGETS
Posted by daen at 06:47 PM
June 22, 2005
The hat-trick ...
OK, we got the Schering AG deal yesterday (pdf).
And still they keep coming ...
Big Pharma companies are more than ever anxious to find viable lead compounds and consequently are keen to make use of technologies which will give them any kind of an edge, against the targets themselves and the competition. Which is where companies like Nuevolution come into the picture. We claim to be able to find high-affinity binders for pretty much any target you can give us in a timespan measured in months rather than years. I don't know much biology (or chemistry) but from what I can glean from some of the smart cookies at Nuevo, we have developed original - and functional - technology over the last four years in order to do this (including some stunningly impressive software ...)
For me, the really interesting part right now is managing all the data which will inevitably spin off from these collaborations, and keeping it in its rightful place. Fortunately, with enough planning and some careful design and development, delivering this kind of partitioning and security isn't as much of a headache as it was 10 years ago.
Posted by daen at 12:52 AM
June 17, 2005
Cheminformatics software
Working with JOELib and OpenBabel was rewarding, in the sense of being part of a community, but also somewhat frustrating, in part because the on-going development of those packages is, well, on-going.
I have a problem with Java : not the language itself, but rather the need to maintain different oh so many JRE installations depending on the software developers or vendors involved. And maybe I'm just not paying attention enough or I'm looking in the wrong places, but I can't get decent performance out of Java on my Windows XP box, or find IDE tools that I can get along with. If anybody has any ideas why my experience has been so negative, please let me know. Maybe I'm just too lazy or dumb.
We finally went for MDL's software. I like it.
The new V3000 molfiles that MDL/Draw produces contain enhanced stereochemistry information, allowing you to handle unknown, known relative and known absolute stereocentres.
The Direct Oracle cartridges (molecule and reaction) allow you to do substructure searches and so-called flexmatch (similarity) searches directly through SQL. You can get molecules highlighted back from the query. These are the newer parts, actually core elements of Isentris, the replacement for ISIS. The older ISIS components (ISIS/Host, ISIS/Base) look a little tired compared to this whizzy stuff.
The real crown jewels for us are Cheshire and the Cheshire Business Rules Manager (CBRM). Cheshire is a set of tools for handling molecules and reactions in silico, comprising an IDE and an engine driven by a rich and powerful Java-like interpreted language. Cheshire acts on collections, primarily, and uses iterators to traverse them. This is all very sensible and grown up. You can join molecules, delete atoms or bonds, alter stereochemistry information, perform transforms or reactions on molecules or groups of molecules according to templates. In short, everything we needed to do can be done with Cheshire.
The CBRM is a repository for Cheshire scripts, and allows multiple "activation tags" to be associated with each script. So every script in the repository might be associated with the "test" tag, but only those to do with enumerating peptide bonds would be associated with the "enum_peptides" tag. An ActiveX control is provided which lets you programmatically load scripts for a particular activation tag, check and correct molecules, and determine the applied rules.
The CBRM ActiveX control has an annoying bug, which is that it will only work properly under the "US English" (or generally English) regional settings. This is because of the "," and "." being swapped around for decimal places in Denmark, France etc. Very annoying, actually.
My impression after one month of working with the MDL tools is that the software is of high quality, regionalization bugs aside, and the documentation of a very high standard. If you buy ISIS/Host, MDL/Draw, Cheshire, CBRM and the Direct cartridges, you are looking at getting through a good three reams of double sided print if you hard copy all the documentation - which I like to do.
There's one niggle with the 840 page Cheshire manual - there are no contents pages! This might seem like a small detail, but it really isn't. I have had to attach small PostIt notes to mark the chapter divisions. The index is comprehensive, but of course doesn't tell you where the section on atom constants starts, for example.
Other niggles. MDL/Draw doesn't include the sequence editor that ISIS/Draw has. You have to edit the XML config file to get some of the more useful out-of-the-box MDL/Draw functionality working (Sgroup data attachments, for example, and the extended stereochemistry handling). CBRM Administrator context help (actually, any help) is non-existent. Cheshire strips atom aliases (A type fields) from molfiles. Boo.
But these relatively minor things aside, the MDL software will allow us to seriously punch above our weight when it comes to handling our cheminformatics data.
Was it cheap? No. Don't ask. But I believe we would have been hard pressed to get to the same place any other way in the timescale we have to work in (three months) and with the resources we have to work with (two developers).
Posted by daen at 12:42 AM
June 15, 2005
They shoot ... they score!
Two goals in the last three months. That is, Nuevolution now has deals with Novo Nordisk and Biovitrum (pdf links). We now just have to find drug-like lead compounds for both companies. No sweat ...
Now, how about a hat trick for July ...?
Posted by daen at 09:30 PM
March 13, 2005
What a peevish fool was that of Crete/That taught his son the office of a fowl!
Cheminformatician Peter Murray-Rust directly quotes Edward Tufte's Wired essay from September 2003 when he starts one of his presentations with the warning that Power Corrupts; Powerpoint corrupts absolutely.
Tufte himself is of course paraphrasing - who? Marx? "Power corrupts; absolute power corrupts absolutely". But no - to my surprise it turns out to be historian Lord Acton (1834-1902). The full quotation is rather wise and is relevant today:
"Liberty is not a means to a higher political end. It is itself the highest political end...liberty is the only object which benefits all alike, and provokes no sincere opposition...The danger is not that a particular class is unfit to to govern. Every class is unfit to govern...Power tends to corrupt, and absolute power corrupts absolutely."
And the title of this entry (a spurious attempt to link hubris to Office ...) is of course from Henry VI, Part 3: Act V, Scene vi, referring itself to the legend of Dædalus and Icarus.
Posted by daen at 03:58 AM
Registering stereochemistry
Abstract: A new effective algorithm for handling of geometry at chiral centres for the processing of stereochemical structures during their unambiguous registration in databases was designed, programmed and implemented. The chemical and mathematical reasoning behind the algorithm are discussed in detail. Its advantages- in comparison to the methods used so far - are illustrated for the manual as well as for the computer-assisted assignment of stereodescriptors based on the CIP ranking procedure
Molecules 2001, 6, 915-926
Starts off with a review of the history of representing 3D chemical structures in 2D (ie stereochemistry), and an explanation of why chemists do this, followed by the inevitable discussion of the challenges and pitfalls of doing it in software.
Posted by daen at 02:19 AM
January 30, 2005
BIOSYS : Copenhagen's biotechnology and system biology high tech network
Syv højteknologiske netværk styrker forskeres relationer til virksomheder
This network, announced back in November, launches tomorrow with 4MM DKK and the following role call of network partners:
Academic institutions
Danmarks Tekniske Universitet
Københavns Universitet
Århus Universitet
Syddansk Universitet
KVL
Danmarks JordbrugsForskning
Industrial
Aros Applied Biotechnology Aps
Astra Zeneca AB
Bavarian Nordic A/S
Carlsberg Biosector A/S
Chr. Hansen A/S
Danske Slagterier
IBM Denmark
Lundbeck A/S
Novo Nordisk A/S
Novozymes A/S
NsGene A/S
Nuevolution A/S
Sejet Planteforædling I/S
SGI A/S
Topotarget A/S
Posted by daen at 10:17 PM
January 20, 2005
Derek Lowe : In the Pipeline
Derek Lowe's In the Pipeline blog discusses aspects of life in the world of drug discovery. Readable, funny and very relevant for me.
Posted by daen at 11:23 PM
October 28, 2004
Pseudo-random enumeration
Daylight webpage on implementing Knuth's pseudo-random generators.
Posted by daen at 11:45 PM
Chemiïnformatics
Or cheminformatics. Or chemoïnformatics.
Whatever. Read about it here.
Dr Wendy Warr maintains a good list of chem{o|i}informatics-related conferences here.
Posted by daen at 11:00 PM
October 07, 2004
Building OpenBabel under MinGW
1. gettimeofday()
This post on Building GNU Chess 5.07 on MinGW/gcc actually addresses a general problem with MinGW - it doesn't support the gettimeofday() call.
This fix from Anders Carlsson addresses that:
---- In common.h after #include <sys/time>, I added the following:/* These are winbase.h definitions, but to avoid including
tons of Windows related stuff, it is reprinted here */
typedef struct _FILETIME {
unsigned long dwLowDateTime;
unsigned long dwHighDateTime;
} FILETIME;
void __stdcall GetSystemTimeAsFileTime(FILETIME*);
void gettimeofday(struct timeval* p, void* tz /* IGNORED */);---- and into main.c, I put the actual gettimeofday function:
void gettimeofday(struct timeval* p, void* tz /* IGNORED */){
union {
long long ns100; /*time since 1 Jan 1601 in 100ns units */
FILETIME ft;
} _now;GetSystemTimeAsFileTime( &(_now.ft) );
p->tv_usec=(long)((_now.ns100 / 10LL) % 1000000LL );
p->tv_sec= (long)((_now.ns100-(116444736000000000LL))/10000000LL);
return;
}----
Anders's original post was in the Redhat GDB mailing list.
2. rindex()
rindex() is unresolved ...
Danny Smith has this to say on the MinGW forum on SourceForge:
index, rindex are non-ANSI version of strchr. strrchr respectivley. msvcrt.dll exports only the ANSI names. Change the references to the non-ANSI names to strchr and strrchr ...
3. Still working on it ... currently having problems with resolving stdcall namemangled GetSystemTimeAsFileTime()
...
Posted by daen at 01:17 AM
August 26, 2004
Indexing Office (Word, Excel, PDF) documents in Plone
Zope.org - Indexing Office (Word, Excel, PDF) documents using ZAAPlugins
Posted by daen at 03:56 PM
August 22, 2004
Molecular Discovery Ltd
The homepage of Molecular Discovery Limited - ALMOND, GRID and Volsurf software.
Dr. Massimo Baroni is the Chief Scientific Officer and the scientist responsible for the Company's products.
Dr. Silvio Mecucci is Head of ADME technology
Dr. Riccardo Vianello is Head of Metabolism technology
Dr. Gianluca Sforna is Head of Communication technology
Dr. Ismael Zamora is Head of project management
Prof. Gabriele Cruciani from the Laboratory for Chemometrics and Cheminformatics at the University of Perugia
Dr. Manuel Pastor from the GRIB at IMIM/UPF in Barcelona
Prof. Peter Goodford from LMB, Oxford, UK.
Prof. Tudor Oprea from Sunset Molecular Discovery LLC
Posted by daen at 11:27 PM
August 17, 2004
Bangalore Bio
A link to the Bangalore Biotech website.
Posted by daen at 10:59 AM
August 03, 2004
Global Genomics AB
Posted by daen at 11:01 AM
July 09, 2004
Recursive Partitioning
Posted by daen at 12:31 AM
June 21, 2004
Chemoinf.com - cheminformatics portal
Posted by daen at 01:05 AM
June 20, 2004
COSMAS : (Chem) -informatics
Posted by daen at 10:04 PM
May 28, 2004
Evolutionary/genetic algorithms in computer-aided molecular design
Evolutionary Algorithms in Computer-Aided Molecular Design
Posted by daen at 12:14 AM
May 24, 2004
SMARTS : carboxylic acid & amine groups
Carboxylic acid
[CX3](=O)[OX2H1]
Amine
[NX3;H2,H1;!$(NC=O)]
From here.
Posted by daen at 11:55 PM
SMARTS
Posted by daen at 07:06 PM
May 23, 2004
RmiJdbc - Type 3 JDBC driver for MS Access
RmiJdbc is a bridge which allows remote access to JDBC drivers using RMI and the Sun-supplied JDBC-ODBC bridge. This link describes in further detail how to connect to MS Access remotely ... Sun describe this in the JDBC FAQ number 5.
Posted by daen at 11:25 PM
May 02, 2004
JOELib
Posted by daen at 10:23 PM
Ghemical
Posted by daen at 10:21 PM
April 28, 2004
Netvault : removing virtual drives
NetVault users: remove virtual drives
Posted by daen at 02:57 PM
April 27, 2004
APC UPS Smart Protocol
Network UPS Tools: APC's smart protocol
I especially like the comment "Sent when the UPS returns from an abnormal condition where ? was sent, but not a turn-on."
Posted by daen at 12:55 PM
Computerstore DK
Posted by daen at 12:16 AM
April 25, 2004
Codessa Pro Chemical Descriptors (QSAR/QSPR)
Posted by daen at 01:20 AM
April 20, 2004
Genetic debugging
"The genome wasn't designed by a computer programmer, from top to bottom. It keeps evolving all the time. There are bits of the genome and RNA molecules that are probably not doing much. Maybe they did once, but they don't now. Or maybe they're evolving a function."
(From BBC NEWS | Science/Nature | Scientists decipher 21,000 genes)
Hmm ... sounds like the genome was designed by a hacker to me ...
Posted by daen at 11:36 PM
Making Exchange folders available in File Explorer with IFS
Get IT Done: Access Exchange public folder data outside of Outlook - TechRepublic
Posted by daen at 11:03 PM
KC's Exchange + Outlook tips
Posted by daen at 04:34 PM
April 18, 2004
Exchange Workflow Designer
Download details: Workflow Designer for Exchange
Posted by daen at 11:34 PM
More logit curves (ELISA)
Posted by daen at 10:01 PM
Multinomial and conditional logit
Categorical Analysis - Models for Unordered Multiple Choices
Posted by daen at 09:41 PM
Logit curves (not shown)
How to obtain reproducible quantitative ELISA results
Posted by daen at 05:01 PM
April 14, 2004
The MLP calculation
Posted by daen at 05:15 PM
BioByte ClogP
BioByte ClogP%u2122 Introduction
Posted by daen at 05:11 PM
CADCOM lipophilicity
Posted by daen at 05:05 PM
April 05, 2004
Graph searching
1. Build query graph.
2. Enumerate unique paths through query graph up to path length 4.
3. Do the same for the search graphs.
4. List combinations of paths to uniquely traverse query graph.
5. Drop those search graphs that don't match in number of enumerated paths.
6. Finally match, join and trim the search graph paths which match the query graph paths.
Posted by daen at 12:46 AM
April 04, 2004
Graph searching etc
Index of /sigs/sigmod/pods/tut/
(See sh.ppt)
Posted by daen at 09:49 PM
SMILES syntax
[atom]bond[atom] etc
atom : ‘[‘ <mass> symbol <chiral> <hcount> <sign<charge>> <‘:’class> ‘]’
;
bond : <empty> | ’-’ | ‘=‘ | ‘#’ | ‘:’ | ‘.’
;
Common elements, in the organic subset B,C,N,O,P,S,F,Cl,Br,I, in their lowest common valence state(s), can be written without brackets. If bonds are omitted, they default to single or aromatic, as appropriate, for juxtaposed atoms.
Posted by daen at 08:52 PM
April 02, 2004
Chemical bond graphs
Computer representation of chemical bonds
Posted by daen at 12:55 AM
March 03, 2004
Danish HPLC forum
The Danish HPLC forum (http://www.hplc-forum.dk) is a new initiative designed to encourage discussion around HPLC products used in Denmark, such as Waters MassLynx, Millennium and Empower. Membership is free.
Posted by daen at 04:16 PM
February 12, 2004
EMBOSS : Input sequence formats, with a link to a description of ABI file format
This page, titled "EMBOSS: Sequence Formats" contains a link to a zip file on an FTP server at CalTech which contains a description of the ABI file format (abi.txt). It's the only description of it I've so far found.
Posted by daen at 12:16 AM
February 11, 2004
Combinatorial Chemistry & HTS : sample issue (5:2 - March 2002)
This sample edition of Combinatorial Chemistry & High Throughput Screening by Bentham Science Publishers has a number of interesting articles on combinatorial libraries:
"A Novel Approach to Combinatorial Library Design"
"Rational Principles of Compound Selection for Combinatorial Library Design"
"A Probabilistic Approach to High Throughput Drug Discovery"
"Optimization of Focused Chemical Libraries Using Recursive Partitioning"
Posted by daen at 10:52 PM
February 09, 2004
Bayesian analysis of combinatorial libraries?
Probabilistic Receptor Potentials
Posted by daen at 04:44 PM
Installing Oracle 9i on RedHat 9.0
Posted by daen at 01:44 AM
January 08, 2004
SMILES for chemists
SMILES is a simple yet comprehensive chemical nomenclature. The SMILES Tutorial provides a comprehensive introduction to the language.
For example, the structure of L-alanine ...
can be represented as N[C@@H](C)C(=O)O as a SMILES code.
Posted by daen at 11:07 AM
MS Project info
Posted by daen at 02:11 AM
December 01, 2003
AGREP - an Approximate GREP
Posted by daen at 10:39 PM
November 29, 2003
Exact sequence matching algorithms
Brute Force algorithm
Deterministic Finite Automaton algorithm
Karp-Rabin algorithm
Shift Or algorithm
Morris-Pratt algorithm
Knuth-Morris-Pratt algorithm
Simon algorithm
Colussi algorithm
Galil-Giancarlo algorithm
Apostolico-Crochemore algorithm
Not So Naive algorithm
Boyer-Moore algorithm
Turbo BM algorithm
Apostolico-Giancarlo algorithm
Reverse Colussi algorithm
Horspool algorithm
Quick Search algorithm
Tuned Boyer-Moore algorithm
Zhu-Takaoka algorithm
Berry-Ravindran algorithm
Smith algorithm
Raita algorithm
Reverse Factor algorithm
Turbo Reverse Factor algorithm
Forward Dawg Matching algorithm
Backward Nondeterministic Dawg Matching algorithm
Backward Oracle Matching algorithm
Galil-Seiferas algorithm
Two Way algorithm
String Matching on Ordered Alphabets algorithm
Optimal Mismatch algorithm
Maximal Shift algorithm
Skip Search algorithm
KMP Skip Search algorithm
Alpha Skip Search algorithm
Posted by daen at 01:44 AM
November 17, 2003
Online Lectures in Bioinformatics, Max Planck Institute
The Max Planck Institute for Molecular Genetics has a useful series of online lectures in bioinformatics here complete with exercises and answers. There's a section on Smith-Waterman and other sequence matching algorithms.
Posted by daen at 11:21 PM
October 31, 2003
De Søde Liv
Next Sunday, my company is off to Rome for a week. All of us. What a lark!
Some of us went to see La Dolce Vita at the Danish Film Institute's Cinemateket on Tuesday night. A great film (especially the part with Anita Ekberg) but 173 minutes without a break is a lot to ask from an audience, Mr Fellini.
Posted by daen at 11:29 AM
October 09, 2003
Nuevolution raises $15 million
NUEVOLUTION A/S RAISES $ 15 MILLION IN FIRST CLOSE OF SERIES B EQUITY FINANCING
Copenhagen, Denmark – October 9, 2003 – Nuevolution A/S a privately held drug discovery company today announced that the Company has raised $15 million in the first closing of a Series B equity financing.
This second round of financing was led by Scandinavian Life Science Venture, and brings to $ 24 million the total funds raised since the Company’s founding in May 2001. The Company intends to raise additional funds through a second closing.
Not bad for a 30 month old company with 30 employees. Champagne and Belgian chocolates all round, then heads down in the labs and back to the phones to raise the next tranche ...
Read the full press release here (110Kb PDF).
Posted by daen at 11:23 PM
October 08, 2003
Biotech & Genetic Engineering
This link to biotechnology at Colorado State Uni is interesting:
Introduction and Background
Overview of Biotechnology and Genetic Engineering
Review of Nucleic Acid and Protein Chemistry
DNA Technology: Manipulating and Characterizing Nucleic Acids
Gel Electrophoresis of DNA and RNA
Restriction Endonucleases and DNA Modifying Enzymes
Vectors and Hosts: Plasmids, Phage and Bacteria
Nucleic Acid Hybridization
Polymerase Chain Reaction
DNA Sequencing and DNA Synthesis
Purifying and Manipulating Nucleic Acids
Molecular Cloning
Overview of Cloning
Cloning cDNAs
Cloning and Characterizing Genes
Expression of Recombinant Proteins
Expressing Recombinant Proteins in Bacteria
Recombinant Protein Expression in Eucaryotic Cells
Specific Mutagenesis
Protein Engineering
Applications of DNA Technology
Diagnostics
Vaccines
Bioremediation
Genetic Engineering of Plants
Genetic Engineering of Animals
Molecular Approaches to Evolution, Archeology and Paleontology
RNA Technology
Posted by daen at 06:55 PM
September 26, 2003
TS connection problems
Posted by daen at 03:37 PM
September 15, 2003
More Linux U320 drivers
Useful page with AIC79xx driver update disk images for various RedHat versions from 7.x to AS 2.1 ... Also available as RPMs and TARs.
Posted by daen at 04:30 PM
September 08, 2003
RedHat 8.0 U320 aic79xx driver
Joy. Rapture. The up-to-date driver. Now my Maxtor Atlas 10K IV can talk at 320Mb/s to my AIC-7902 without getting its knickers in a twist ...
Posted by daen at 10:33 PM
August 28, 2003
Rendering sequence data graphically with BioPerl
Abstract
"This HOWTO describes how to render sequence data graphically in a horizontal map. It applies to a variety of situations ranging from rendering the feature table of a GenBank entry, to graphing the positions and scores of a BLAST search, to rendering a clone map. It describes the programmatic interface to the Bio::Graphics module, and discusses how to create dynamic web pages using Bio::DB::GFF and the gbrowse package"
Thanks to Lincoln Stein for this
Posted by daen at 11:32 PM
July 04, 2003
Online chemistry course
Organic Chemistry (Francis A. Carey) : Contents
Needs Chime from MDL
Posted by daen at 01:21 AM
July 01, 2003
Solvents
Posted by daen at 03:04 PM
June 26, 2003
A Python course in Bioinformatics
Python course in Bioinformatics
This course is designed for biologists who already have some programming knowledge, in other languages such as perl or C. ... This course can be considered a complement to the Biopython tutorial, and what's more often refers to it, by bringing practical exercises using these components.
Posted by daen at 07:07 PM
EMBOSS (The European Molecular Biology Open Software Suite) fuzznuc application
fuzznuc uses PROSITE style patterns to search nucleotide sequences.
Perfect!
Posted by daen at 12:46 AM
June 24, 2003
Biological sequence alignment : presentations
Biological sequence comparison
Powerpoint presentation, with useful commentary on Needleman-Wunsch and Smith-Waterman alignment algorithms.
BioLinux : Bioinformatics and Linux
Link to .PDF on implementing Smith-Waterman algorithm in Perl.
Posted by daen at 12:30 AM
June 18, 2003
DNA sequencer output and sequence file formats
Phred/Phrap and Consed are industrial strength sequence assembly programs that are currently used for LARGE sequencing projects at the genome centers. If you are sequencing a few thousand nucleotides, you don't need this program. Use something like SeqMan, Sequencher, or GCG. If you are assembling genomes or thousands of ESTs, then this is the program for you. However, Phred and Phrap are not for the faint of heart. There is a significant learning curve.
PHRED - Base-Calling Software with Quality Information
Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Phred can read trace data from SCF files and ABI model 373 and 377 DNA sequencer chromat files, automatically detecting the file format. After calling bases, phred writes the sequences to files in either FASTA format, the format suitable for XBAP, PHD format, or the SCF format. Quality values for the bases are written to FASTA format files or PHD files, which can be used by the phrap sequence assembly program in order to increase the accuracy of the assembled sequence.
PHRAP - sequence-assembly program
Phrap ("phragment assembly program", or "phil's revised assembly program") is a program for assembling shotgun DNA sequence data. Some of its key features are: (1) allows use of entire read, not just highest quality part; (2) uses a combination of user-supplied and internally computed data quality information to improve accuracy of assembly in the presence of repeats; (3) constructs contig sequence as a mosaic of the highest quality parts of reads, rather than a consensus. Phrap does not provide editing or viewing capabilities; these are available with consed or phrapview
BioAfrica - Bioinformatics Unit for HIV Research
Mostly HIV related, but includes some useful examples of sequence file formats: GenBank, FASTA, Nexus (PAUP) and Phylip.
GeneStudio, Inc. Molecular Biology Software
SeqVerter™ - standalone version
SeqVerter™ is a free sequence file format conversion utility by GeneStudio, Inc. SeqVerter encapsulates a small subset of the features offered by the GeneStudio™ Pro suite of programs. While the standalone SeqVerter is a simple dialog-based utility, the free SeqVerter component of the GeneStudio Pro suite adds sophisticated viewers and sequence formatting functions, including a viewer for automatic DNA sequencer chromatogram files (traces).
Clark Tibbetts's ABI Data format Paper
Raw Data File Formats, and the Digital and Analog Raw Data Streams of the ABI PRISM 377 DNA Sequencer.
Has a link to 35 page .ps file presumably describing the format (I haven't got Ghostscript or Ghostview installed, so I can't tell at the mo'). Update, 24 June 2003 -- Yes, this is the ABI 377 data file format ... and here is the link to Ghostscript and Ghostview, which you will need to view and print PostScript on Windows ...
Posted by daen at 11:39 PM
June 04, 2003
Samba - the fatal dance of Unix and Windows
SAMBA - opening windows to a wider world
Don't forget about smbpasswd!
Posted by daen at 03:17 PM
June 03, 2003
Danish bioinformatics tools
SEQtools - a software package for DNA sequence analysis
Thanks to Søren W Rasmussen for this link.
SEQtools is a comprehensive program package for batch handling and analysis of nucleotide and protein sequences. The program includes a series of trivial functions to help you carry out common operations. In addition SEQtools will assist you with more demanding operations like unattended blast search and result-parsing with hundreds of sequences.
Special functions are included for design of microarray gene expression analysis experiments, for expression analyses with the SAGE procedure and for managing small EST projects. Utilities are included for primer design and ordering, renaming files, creating codon usage tables, building local searchable databases, aligning nucleotide and protein sequences, comparing sequences and a lot more...
Posted by daen at 11:13 PM
February 16, 2003
Office life : 21 years on, and still relevant ...
Life in Hell: How to Kill Eight Hours a Day and Still Keep Your Job
Matt Groening ... Life in Hell ... genius.
Posted by daen at 12:26 AM