mp3producer 2.60
DNA BASER 2.60
Visit us for updated info: http://www.DNABaser.com DNA Baser Assembler is easy to use software for simple and batch DNA sequence assembly, DNA sequence analysis, contig editing, metadata integration and mutation detection. It also offers a powerful chromatogram viewer/editor. The truly user-friendly interface makes DNA Baser the best choice for DNA contig assembly. For more details, see the DNA BASER Features page. File formats supported are abi, scf and seq (or FASTA). Features: end clip, export,auto trim... more>>
DNA BASER - Visit us for updated info: http://www.DNABaser.com
DNA Baser Assembler is easy to use software for simple and batch DNA sequence assembly, DNA sequence analysis, contig editing, metadata integration and mutation detection. It also offers a powerful chromatogram viewer/editor. The truly user-friendly interface makes DNA Baser the best choice for DNA contig assembly. For more details, see the DNA BASER Features page.
Why is DNA Baser Assembler special?
Any software company pretends that their product is the best. But lets see for real if DNA Baser can offer you a better proposition. As you will see below we concentrate on adding automatic and batch functions to our product in order to decrease the time. Additional to this, DNA Baser is available at a "kill your competition" price.
Forget about manually trimming the low quality ends of your sequences. DNA Baser Assembler will do it for you!
Do you think you need weeks to assemble hundreds of contigs? What about doing this in minutes? DNA Baser is the only software that can automatically detect and assemble sequences belonging to the same contig based on their filename.
Do you think that is necessary to spend more than 20 minutes to correct discrepancies and mismatches in every contig? Wrong! DNA Baser is the first software which can make correct suggestions in at least 98% of cases.
Have you ever wondered how others laboratories afford to have sequence assembly software in EVERY computer? Simple! They dont spend thousands of dollars for each license. They use DNA Baser Assembler. DNA Baser is affordable, has no annual maintenance fees, technical support is included in price and you have instant access to your key, right after purchase.
You dont have to fill in and submit forms in order to get a trial version. If you want to try it, you can download and install it in less than one minute. No personal data or registration process is required. The trial version is fully functional.
DNA BASER Assembler offers a smart navigation system that takes you to the location of each sequence ambiguity / mutation with a single click.
Enhancements:
Version 2.60
New: Metadata and batch metadata integration.
New: Button to open Windows Explorer in contigs folder, after sequence assembly.
New: Remove vectors from single chromatograms.
New: SEQUENCE ANALISYS - mark al bases with a confidence level (QV) below a specified threshold, in red.
New: Batch convert from chromatogram to Fasta with vector removal and automatic metadata integration.
New: Resizable chromatograms.
Full support for low quality sample ends editing.
100% compatible with Mac via Parallels/Bootcamp/VMWare.
Improved handling of corrupted/invalid ABI/SCF files.
Improved contig editor.
Improved file association.
Improved Assemble to reference.
Improved log window.
Improved file handling: Before starting the contig, check if all files in the JobList are valid. Invalid samples are automatically removed from Job List so the assembly process can continue without human intervention. Build a list of invalid files and report it.
Improved user interface: new toolbar, improved embedded help, interactive help, workflow...
Improved sample viewer: Mark as trusted/un-trusted can now be used also in Sample viewer window
New: Show error message while trying to open empty/invalid FASTA files
Improved: Correctly handle multiple contigs resulted when assembling to a reference.
Improved: menu Save as Fasta/Seq/Scf was replaced with Save all as... and Save selected as.... Now the user can choose where to save the file.
Version 2.10
Batch assembly. Thousand of contigs can be assembled at once.
System Requirements:CPU: 333MHz, 64MB RAM, Video 1024x768, 2MB HDD free space<<less
Clean_Mail 2.60
Clean_Mail provides scripts to help maintain mail spool files on a large system. more>>
Clean_mail is a series of shell and Perl scripts that help a system administrator maintain mail spool files on a large system.
They offer deleting of old mails, backup, deleting of spam, automatic mails to users, etc.
What does Clean_Mail do ?
If you works with a version earlier than 2.59, you must not run several session of Clean_Mail at the same time. The different parts of the programm communicate with files and it would have impredictable results.
There is now a lock file (clean_mail.lock in /tmp) that avoid risks of data loss.
This software is particularly useful when a lot of users does not erase their mails from the server.
The program can manage backups, optional automatic mails to users, and anti-spam mode.
cgichk 2.60
cgichk is a Web vulnerability tool. more>>
I originally came upon a CGI vulnerability scanning late last year and for fun, decided to rewrite it (Im a sucker for organizing code I didnt write to my own style.) I added more and more to it, and decided to add in some curiousity things to search for, besides the already built in files.
This was NEVER intended to be a tool for being an asshole with. Im just a nosy, curious bastard and have created a tool to automate the search because Im infinitely lazy.
This program does nothing that a person with two hands and a brain couldnt do.
Enhancements:
- Added an option (-H) to retrieve the HTTP header and then quit.
- Began to wonder if this app would be better off using Perl, and then decided against it.
- Added some new targets (well, php versions of old specific targets).
- Added option (-I) to NOT look inside 200s for 404 type strings.
Text::MacroScript 1.38
Text::MacroScript is a macro pre-processor with embedded perl capability. more>>
SYNOPSIS
use Text::MacroScript ;
# new() for macro processing
my $Macro = Text::MacroScript->new ;
while( ) {
print $Macro->expand( $_ ) if $_ ;
}
# Canonical use (the filename improves error messages):
my $Macro = Text::MacroScript->new ;
while( ) {
print $Macro->expand( $_, $ARGV ) if $_ ;
}
# new() for embedded macro processing
my $Macro = Text::MacroScript->new( -embedded => 1 ) ;
# Delimiters default to
# or
my $Macro = Text::MacroScript->new( -opendelim => [[, -closedelim => ]] ) ;
while( ) {
print $Macro->expand_delimited( $_, $ARGV ) if $_ ;
}
# Create a macro object and create initial macros/scripts from the file(s)
# given:
my $Macro = Text::MacroScript->new(
-file => [ local.macro, ~/.macro/global.macro ]
) ;
# Create a macro object and create initial macros/scripts from the
# definition(s) given:
my $Macro = Text::MacroScript->new(
-macro => [
[ MAX_INT => 32767 ],
],
-script => [
[ DHM2S =>
[
my $s = (#0*24*60*60)+(#1*60*60)+(#2*60) ;
"#0 days, #1 hrs, #2 mins = $s secs"
],
],
-variable => [ *MARKER* => 0 ],
) ;
# We may of course use any combination of the options.
my $Macro = Text::MacroScript->new( -comment => 1 ) ; # Create the %%[] macro.
# define()
$Macro->define( -macro, $macroname, $macrobody ) ;
$Macro->define( -script, $scriptname, $scriptbody ) ;
$Macro->define( -variable, $variablename, $variablebody ) ;
# undefine()
$Macro->undefine( -macro, $macroname ) ;
$Macro->undefine( -script, $scriptname ) ;
$Macro->undefine( -variable, $variablename ) ;
# undefine_all()
$Macro->undefine( -macro ) ;
$Macro->undefine( -script ) ;
$Macro->undefine( -variable ) ;
# list()
@macros = $Macro->list( -macro ) ;
@macros = $Macro->list( -macro, -namesonly ) ;
@scripts = $Macro->list( -script ) ;
@scripts = $Macro->list( -script, -namesonly ) ;
@variables = $Macro->list( -variable ) ;
@variables = $Macro->list( -variable, -namesonly ) ;
# load_file() - always treats the contents as within delimiters if we are
# doing embedded processing.
$Macro->load_file( $filename ) ;
# expand_file() - calls expand_embedded() if we are doing embedded
# processing otherwise calls expand().
$Macro->expand_file( $filename ) ;
@expanded = $Macro->expand_file( $filename ) ;
# expand()
$expanded = $Macro->expand( $unexpanded ) ;
$expanded = $Macro->expand( $unexpanded, $filename ) ;
# expand_embedded()
$expanded = $Macro->expand_embedded( $unexpanded ) ;
$expanded = $Macro->expand_embedded( $unexpanded, $filename ) ;
This bundle also includes the macro and macrodir scripts which allows us to expand macros without having to use/understand Text::MacroScript.pm, although you will have to learn the handful of macro commands available and which are documented here and in macro. macro provides more documentation on the embedded approach.
The macroutil.pl library supplied provides some functions which you may choose to use in HTML work for example.
Remote Python Call 2.60
RPyC stands for Remote Python Call, a pun over remote procedure call. more>>
Learning the lowlevel of the python language attempting to improve pyinvoke by making the entire protocol symmetrical. This means the client can make requests to the server, and the server can reply with requests of its own (the client is also a server on its own). This typically means using callback functions.
The RPyC package comes with a full demo, showing (or showing-off) many of its features. As i said, its completely transparent and symmetrical, so you can write code just as you would write in the case of normal python programs.
demo 1 -- a simple client demo
# import the client
from Rpyc.Client import RpycSocketClient
# `hostname` is the name of the host running an Rpyc server
# the port parameter is optional
c = RpycSocketClient("hostname")
# now we are connected and can start messing around with stuff on the server
for filename in c.modules.os.listdir("/tmp"):
print "found file", filename
Enhancements:
- This release adds DeliveringNamespace, LoginError (instead of tlslites internal errors), __version__, deliver (the counterpart of obtain, which can now deliver and obtain functions as well), and isproxy (to test whether an object is a proxy).
- It improves memory consumption with __slots__ and the isinstance/issubclass mechanism.
Wolfenstein: Enemy Territory Update 2.60
Wolfenstein: Enemy Territory is a Multiplayer Online First Person Shooter. more>>
Featuring multiplayer support for as many as 64 players, Wolfenstein: Enemy Territory challenges gamers to the ultimate test of teamwork and strategy. Each of the five character classes is critical to a teams ultimate victory or defeat on the battlefield. The Covert Operative class allows players to steal uniforms, perform reconnaissance and gain access to enemy positions. While, the Engineer allows the Axis and Allied teams to lay and diffuse mines as well as build battlefield bridges, towers, forward command bases and other improvements in the midst of combat to gain advantages for their team.
Wolfenstein: Enemy Territory further online players the option to slug it out in the intense Team Last-Man-Standing game mode, where squad-mates cooperate to ensure their team has the last surviving man on the battlefield. With new game modes, character classes, weaponry, and added tactical skills, Wolfenstein: Enemy Territory will keep gamers in the trenches for hours.
Cromfs 1.5.2
Cromfs is a compressed read-only filesystem for Linux. more>>
Version restrictions:
- Filesystem is write-once, read-only. It is not possible to append to a previously-created filesystem, nor it is to mount it read-write.
- Max filesize: 2^64 bytes (16777216 TB), but 256 TB with default settings.
- Max number of files in a directory: 2^30 (smaller if filenames are longer, but still more than 100000 in almost all cases)
- Max number of inodes (all files, dirs etc combined): 2^60, but depends on file sizes
- Max filesystem size: 2^64 bytes (16777216 TB)
- There are no "." and ".." entries in directories.
- mkcromfs is slow. You must be patient.
- The cromfs-driver has a large memory footprint. It is not suitable for very size-constrained systems.
- Ownerships are not saved.
- Maximum filename length: 4095 bytes
Main features:
- Data, inodes, directories and block lists are stored compressed
- Duplicate inodes, files and even duplicate file portions are detected and stored only once
- Especially suitable for gigabyte-class archives of thousands of nearly-identical megabyte-class files.
- Files are stored in solid blocks, meaning that parts of different files are compressed together for effective compression
- Most of inode types recognized by Linux are supported (see comparisons).
- The LZMA compression is used. In the general case, LZMA compresses better than gzip and bzip2.
- As with usual filesystems, the files on a cromfs volume can be accessed in arbitrary order; the waits to open a specific file are small, despite the files being semisolidly archived.
GRhino 0.16.0
GRhino is an Othello/Reversi with a good AI. more>>
GRhino is currently under development and a new version is available occasionally. The latest version is 0.15.0. You can download it here.
What distinguish GRhino from most other Othello games is that GRhino will be targeted for experienced Othello players. Strong AI is the main focus with some additional good, useful features (like an endgame solver) is planned.
The ultimate target strength of the AI is that it should be able to beat the best human player at the highest difficulty level. Beating Logistello (the strongest program available) is not in the plan.
Some important AI infrastructure has been finished. Pattern evaluator and open book are mostly done but still requires some further optimization and data file compression.
Multi prob-cut to speedup the AI is still missing so it still has a limit on its game strength but this mostly affects playing against other strong AI out there. The main focus for current development is about user interface and features.
Main features:
- End game search. It can now solve the exact score (in about 20 sec on P-133) at around 15 empties and Win-Loss-Draw at a slightly higher number of empties.
- Move ordering.
- Start game from known openings.
- Display opening name.
- A decent pattern-based evaluation with parity knowledge.
- A decent open book with opening variations allowed.
- Browse IOS and GGS format game file.
Enhancements:
- Add Edit board feature.
- Fix game log bug that prevents GRhino to open its own game log.
- Fix help file installation issue. Report and patch from Michel Salim.
- Add desktop icon. Patch from Michel Salim.
- Add grhino.desktop (not installed automatically yet). Patch from Michel Salim.
- Update to Autoconf 2.60, gettext 0.16. This should fixes gettext detection failure in configure script.
Number::Bytes::Human 0.07
Number::Bytes::Human is a Perl module that can convert byte count to human readable format. more>>
SYNOPSIS
use Number::Bytes::Human qw(format_bytes);
$size = format_bytes(0); # 0
$size = format_bytes(2*1024); # 2.0K
$size = format_bytes(1_234_890, bs => 1000); # 1.3M
$size = format_bytes(1E9, bs => 1000); # 1.0G
# the OO way
$human = Number::Bytes::Human->new(bs => 1000, si => 1);
$size = $human->format(1E7); # 10MB
$human->set_options(zero => -);
$size = $human->format(0); # -
THIS IS ALPHA SOFTWARE: THE DOCUMENTATION AND THE CODE WILL SUFFER CHANGES SOME DAY (THANKS, GOD!).
This module provides a formatter which turns byte counts to usual readable format, like 2.0K, 3.1G, 100B. It was inspired in the -h option of Unix utilities like du, df and ls for "human-readable" output.
From the FreeBSD man page of df: http://www.freebsd.org/cgi/man.cgi?query=df
"Human-readable" output. Use unit suffixes: Byte, Kilobyte,
Megabyte, Gigabyte, Terabyte and Petabyte in order to reduce the
number of digits to four or fewer using base 2 for sizes.
byte B
kilobyte K = 2**10 B = 1024 B
megabyte M = 2**20 B = 1024 * 1024 B
gigabyte G = 2**30 B = 1024 * 1024 * 1024 B
terabyte T = 2**40 B = 1024 * 1024 * 1024 * 1024 B
petabyte P = 2**50 B = 1024 * 1024 * 1024 * 1024 * 1024 B
exabyte E = 2**60 B = 1024 * 1024 * 1024 * 1024 * 1024 * 1024 B
zettabyte Z = 2**70 B = 1024 * 1024 * 1024 * 1024 * 1024 * 1024 * 1024 B
yottabyte Y = 2**80 B = 1024 * 1024 * 1024 * 1024 * 1024 * 1024 * 1024 * 1024 B
I have found this link to be quite useful:
http://www.t1shopper.com/tools/calculate/
If you feel like a hard-drive manufacturer, you can start counting bytes by powers of 1000 (instead of the generous 1024). Just use bs => 1000.
But if you are a floppy disk manufacturer and want to start counting in units of 1024000 (for your "1.44 MB" disks)? Then use bs => 1_024_000.
If you feel like a purist academic, you can force the use of metric prefixes according to the Dec 1998 standard by the IEC. Never mind the units for base 1000 are (B, kB, MB, GB, TB, PB, EB, ZB, YB) and, even worse, the ones for base 1024 are (B, KiB, MiB, GiB, TiB, PiB, EiB, ZiB, YiB) with the horrible names: bytes, kibibytes, mebibytes, etc. All you have to do is to use si => 1. Aint that beautiful the SI system? Read about it:
http://physics.nist.gov/cuu/Units/binary.html
You can try a pure Perl "ls -lh"-inspired command with the one-liner, er, two-liner:
$ perl -MNumber::Bytes::Human=format_bytes
-e printf "%5s %sn", format_bytes(-s), $_ for @ARGV *
Why to write such a module? Because if people can write such things in C, it can be written much easier in Perl and then reused, refactored, abused. And then, when it is much improved, some brave soul can port it back to C (if only for the warm feeling of painful programming).
OSSP cfg 0.9.11
OSSP cfg is a ISO-C library for parsing arbitrary C/C++-style configuration files. more>>
This means the configuration syntax has a recursive structure and allows you to create configurations with arbitrarily-nested sections.
The configuration syntax also provides complex single/double/balanced quoting of tokens, hexadecimal/octal/decimal character encodings, character escaping, C/C++ and shell-style comments, etc.
The library API allows importing of a configuration text into an Abstract Syntax Tree (AST), traversing the AST, and optionally exporting the AST again as a configuration text.
Enhancements:
- The build environment has been upgraded to GNU libtool 1.5.22, GNU shtool 2.0.6, and GNU autoconf 2.60.
OSSP shiela 1.1.7
Shiela is an access control and logging facility for use with the Concurrent Versions System (CVS). more>>
This way OSSP shiela provides access control on a path and branch basis to particular repository users and user groups. Additionally, repository operations are monitored, accumulated and logged.
The lookout of logging messages can be configured individually on a module path and branch basis and messages can be both saved to files and/or delivered by Email.
Enhancements:
- This release fixes an "arbitrary shell command execution" security bug caused by missing shell command argument escaping for user supplied arguments (CVE-2006-3633).
- The build environment was upgraded to GNU shtool 2.0.6 and GNU autoconf 2.60.
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