Recent Posts Tagged With programming

• R script to filter probesets with log-expression values below the lowest spike-in

  Posted on Wednesday January 27th, 2010 at 06:44 am in programming, science, bioinformatics, r, filter, microarray, affymetrix, log-expression, probeset, spike-in

  Sometimes there is a need to remove all the probesets, which have expression values below the minimal spike-in intensity on the Affymetrix microarray. The reasoning behind this procedure is simple: minimal-expression spike-ins represent the bottom ma...

• Cloud-based bruteforcing, slowloris, and Golang: links

  Posted on Friday November 13th, 2009 at 10:34 am in programming, web, links, Security, misc, mod, apache, Cost, complexity, password, go, ec

  A nice report on the cost of bruteforcing variable-length and variable-complexity passwords using cloud computing services (e.g. Amazon’s EC). There’s a kind of a tutorial in their previous post. Slow DoS attack with just 1 computer again...

• Configuring web-server: for production and for development

  Posted on Sunday October 25th, 2009 at 10:16 am in Software, php, programming, links, development, How-To, production, notepad, web-server

  Production: see http://www.howtoforge.com/how-to-set-up-apache2-with-mod_fcgid-and-php5-on-debian-etch – it is for Debian Etch (which is old-stable), but many of the steps apply equally well to Debian Lenny (current-stable). Also, this is a ver...

• Convenient design and debugging of regular expressions under Linux

  Posted on Saturday October 10th, 2009 at 10:51 am in Software, programming, Linux, notepad, debugging, re, regular expression, *nix, regexp, redet, kodos, txt2regexp

  Regular expressions (regexps) are powerful indeed. But debugging non-trivial regexps is a burden even if you understand how regexps work, and remember most (if not all) regexp syntax. Miscellaneous tools exist to ease this task. This post was inspire...

• Bad memory handling and server stability

  Posted on Monday July 13th, 2009 at 04:29 am in Software, programming, memory, ram, *nix, valgrind, mtrace

  The two graphs below (clickable) are for CPU and RAM use during a period of a program going wild between 23:17 and 23:41 (24+ minutes of server’s downtime). The program was run non-root, it just consumed all the memory it could. It was killed b...

• C: how to specify comparison operators floating precision

  Posted on Thursday June 11th, 2009 at 12:47 pm in programming, How-To, double, precision, comparison, floating, c, float, operator, example

  There is no way I'm aware of to do what the title says. However... I'm sure that you are aware of the fact that floats representation in any programming language is limited by the precision of the internal binary representations. In other words, you ...

• Debugging PHP: Eclipse PDT + XDebug + XDebug helper

  Posted on Sunday June 7th, 2009 at 05:59 pm in Software, php, programming, Firefox, links, development, bug, eclipse, debugging, xdebug, pdt

  Stimulated by a bug in a complex and unfamiliar web PHP application with heaps of custom tweaks by other programmers, I decided to try a more professional approach to PHP programming and debugging than the standard var_dump() and family. As a result,...

• GNU make for bioinformatics presentation

  Posted on Friday June 5th, 2009 at 04:37 am in programming, links, make, bioinformatics, presentation

  Giovanni Dall’olio has recently posted a presentation on using make. Although it has “bioinformatics” on the title page, this is a good and very easy to understand make intro. Original post is here....

• Ada GNAT GPL 2009 released

  Posted on Saturday May 30th, 2009 at 04:55 pm in programming, links, download, release, ada, gnat

  We are pleased to announce the release of GNAT GPL 2009, the Ada Toolset for Academic users and FLOSS developers. It introduces many new features including: - Ability to generate byte code for the JVM - Improved support for the .NET Framework - Addit...

• WordPress and Google Analytics external nofollow problem in comment links

  Posted on Friday February 13th, 2009 at 01:41 pm in Software, php, programming, fix, web, link, wordpress, How-To, cms, problem, comment

  Since some WP release, the comment author's link in comments is broken - it has ' external nofollow' attached straight to the href attribute (which breaks the link). I assume that the problem is caused by Google Analytics, namely the "track outgoing ...

• Git: how to remove file and commit from history

  Posted on Friday February 13th, 2009 at 01:21 pm in programming, links, history, How-To, file, remove, repository, git

  Once I accidentally added circa 300 MiB of archive files to one of my git repositories (which was as small as 5 MiB). I removed those files as soon as I noticed them, but the .git directory still preserved commits with those files, and still occupied...

• ExpressionEngine contact form (email module) spam vulnerability

  Posted on Monday January 26th, 2009 at 03:50 am in Software, php, programming, web, spam, cms, vulnerability, ee, expressionengine

  Yesterday I had a look at mod.email.php - the Email module of ExpressionEngine CMS. It appears that it is very easy to use ExpressionEngine’s contact form (which uses Email module) to send emails to arbitrary addresses - simply put, send spam u...

• Software development schedules

  Posted on Friday November 21st, 2008 at 05:24 pm in Software, programming, software development, schedule, notepad, joel spolsky, evidence-based

  Joel Spolsky has an interesting (and useful) post on evidence-based scheduling, as he calls that approach. The post discusses an approach to estimate project volume and key dates (such as milestones and release) based on prior performance of each of ...

• GNAT GPL 2008 is now available

  Posted on Wednesday June 11th, 2008 at 05:38 pm in programming, ada, gnat

  We are pleased to announce the release of GNAT GPL 2008, the Ada Toolset for Academic users and FLOSS developers. It introduces hundreds of enhancements including: Availability on the Windows .NET platform Upgrade of the debugging engine Improvement...

• Developing reluctant (pessimal) algorithms

  Posted on Saturday April 12th, 2008 at 08:33 pm in programming, humour, reluctant algorithm

  If you had some programming experience - read it here. Otherwise ignore, it’s targeted for a narrow group....

• Instructions on installing libmp3lame-enabled ffmpeg on shared linux hosting

  Posted on Wednesday March 12th, 2008 at 01:25 am in php, programming, shared hosting, ffmpeg, *nix, libmp3lame

  Note: this post is based on the comment by Simon, who generously shared his experience. Step-by-step: Download the compiled ffmpeg with libmp3lame support (direct download links: older version ffmpeg.with.lame and newer version ffmpeg.2007-10-28.wit...

• How to improve MySQL application perfromance

  Posted on Thursday March 6th, 2008 at 08:48 am in programming, MySQL, hints, application, performance, developer, presentation, storage engine

  Juicy presentation, even for seasoned MySQL developers. | View | Upload your own You can also download the PDF of this presentation:...

• SQL injection: RIAA example

  Posted on Saturday February 16th, 2008 at 02:38 am in programming, riaa, notepad, hacked, sql injection

  I know it’s kind of old now, but check this image out: Via webplanet.ru - reddit.com. Share This...

• Python: passing by value vs passing by reference

  Posted on Monday February 11th, 2008 at 10:06 am in programming, python, scope, variable, object, function, by reference, by value

  Note: this a collection of scraps, describing how values (de)referencing works in Python, and describing when your variable is either a value or a reference. Primary source of knowledge for this post (also here). Python passes references-to-objects b...

• Convert MySQL database from one encoding/collation into another

  Posted on Friday February 8th, 2008 at 01:17 pm in php, programming, MySQL, database, convert, notepad, encoding, utf8, collation, latin1

  Most frequent use: convert database from latin1_swedish to utf8_general_ci. Script copy-pasted from: MySQL and UTF-8. Here’s the script itself: (to copy-paste: first click the “Plain text” header; in FF2, RightClick->”Select a...

• CodeCodex: shared online code repository

  Posted on Monday December 10th, 2007 at 03:25 am in programming

  CodeCodex Wiki. Found this one useful when looking for string conversion to uppercase - CodeCodex has it for 10 languages (alas, Ada isn’t among them - but it’s present in tiny pieces here and there, when searching for it at CodeCodex)....

• MySQL: INSERT IF NOT EXISTS syntax

  Posted on Thursday October 18th, 2007 at 08:20 am in programming

  To start: as of the latest MySQL, syntax presented in the title is not possible. But there are several very easy ways to accomplish what is expected using existing functionality. There are two possible solutions: using INSERT IGNORE or REPLACE. Imagi...

• GoDaddy: undocumented 20-second CPU time limit on all executables? (python, ELF, etc)

  Posted on Tuesday October 16th, 2007 at 05:32 am in programming, *nix

  Today, setting up a relatively serious (in CPU resources needed) web-system, I ran into a weird problem of python scripts ending prematurely. After some investigation, it looked like any process which uses up more than 20 seconds of CPU time, is auto...

• Flash countdown video tutorial

  Posted on Thursday September 27th, 2007 at 09:06 am in programming

  Found a good video tutorial on how to create a countdown animation with Flash. Important notice: in my case, if Auto kern was enabled for the dynamic text box, there were no digits visible at all (size of my countdown animation was 120px wide and 186...

• Useful Python looping techniques

  Posted on Wednesday September 26th, 2007 at 04:21 am in programming, python, notepad

  These are all excerpts from the Python documentation. To synchronously and simultaneously loop over two sequences: PLAIN TEXT PYTHON: questions = ['name', 'quest', 'favourite colour'] answers = ['Lancelot', 'the holy grail', 'blue'&...

• How to sort Python dict (dictionary)

  Posted on Wednesday September 26th, 2007 at 01:20 am in programming, python, notepad

  Sample script (copypasted from Well House Consultants training course): click the PLAIN TEXT header for copy-pasteable version PLAIN TEXT PYTHON: #!/usr/local/bin/python   author = {"php":"Rasmus Lerdorf",\     "perl":"L...

• PHP proxy

  Posted on Wednesday September 19th, 2007 at 11:41 am in php, programming, notepad

  PHP proxy is simple but good. I converted it into a proxy-function for one of my projects. Do pay attention to the comments, especially these two: I had issues with this script (and others) returning 0 for the bytesTotal in flash. Basically, the Con...

• MySQL - Python: good MySQLdb tutorial (examples)

  Posted on Friday September 7th, 2007 at 07:32 am in programming, python, notepad

  Andy Dustman gave a presentation on Python and MySQL at the MySQL Users Conference 2005, Santa Clara, CA. The presentation is an excellent collection of examples for those who use the MySQLdb Python module. For the purpose of maintaining a personal...

• Date and time in Python scripts

  Posted on Friday September 7th, 2007 at 07:07 am in programming, python, notepad

  Here’s an excellent description of various methods to handle date and time in Python scripts....

• Elegantly converting Python list into another list with changed items

  Posted on Thursday August 30th, 2007 at 04:06 am in programming, python

  I just had a small problem with my Python script: 1. I have a list of tuples, called records_cache; each tuple looks like this: (note: for copy-pasting, click the PLAIN TEXT box headers) PLAIN TEXT PYTHON: (ensembl_transcript_id, ensembl_gene...