Free blast software for linux

Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s).

SYNOPSIS

use strict;
use Bio::Index::Blast;
my ($indexfile,$file1, $file2);
my $index = new Bio::Index::Blast(-filename => $indexfile,
-write_flag => 1);
$index->make_index($file1, $file2);

my $id;
my $data = $index->get_stream($id);

my $bplite_report = $index->fetch_report($id);
print "query is ", $bplite_report->query, "n";
while( my $sbjct = $bplite_report->nextSbjct ) {
print $sbjct->name, "n";
while( my $hsp = $sbjct->nextHSP ) {
print "t e-value ", $hsp->P,
}
print "n";
}

This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. Note: for best results use strict.

Alien Blaster project is an action-loaded 2D arcade shooter game for up to two players.
alienblaster is an action-loaded 2D arcade shooter game.
Your mission in the game is simple: stop the invasion of the aliens by blasting them.
Simultaneous two-player mode is available.
Main features:
- many aliens to blast
- a big bad boss
- different weapons
- special items
- cooperative mode (2 players playing on 1 computer)
- gamepad/joystick support
- arcade mode with highscore
- open source
- published under GPL
- runs with Windows and Linux

qgreylistrbl is an add-on for qmail.

Now there are a lot of methods against spam, I have combined two of them: greylisting only for dialin nodes and nodes listed on a RBL. NDNs with more than one recipient will be rejected with permanent error messages and without a greylist entry. A test for EHLO/HELO spoofing was added: if a string is obviously spoofed, the connection will be rejected with a permanent error message, without a greylist entry, and advice to RFC2821. You can define a maximum number of recipients per email.

Greylisting returns a temporary SMTP error at the first delivery attempt. Most spam is sent from bulk mailers that dont retry, so these attempts are blocked. Real mail servers will retry later after a temporary error, allowing the message to go through.

Of course cannot all mail be delayed half an hour or longer to our customers. Thats why I have decided to modify the program qgreylist from Jon Atkins. I have added a RBL request to accept emails from not RBL listed nodes and to delay only dialin lines and RBL listed nodes. The script tests the PTR record of each connecting host for a regular expression to detect dialin nodes.

qgreylist from Jon Atkins puts all files in one base dir. qgreylistrbl creates here a directory structure because of performance reasons. The cleanup is now done by a separate cronjob script and not by qgreylistrbl itself, because when there were some ten thousand files inside the mail server nearly stands still.

Most bulk mailers and zombies,too, do not have queue management. They blast that much emails out into the net, they would be swamped with it. An Example: We use a UW-160 Raid 10 for the queue, but the usual zombie out there has only one IDE disc. Beside even a layman would ask why his hard drive was running all the time.

Effect

80% less spam. Yes, truly. No false positives, NO email gets lost.

Usage

qgreylistrbl is a replacement for rblsmtpd by D.J. Bernstein. Simply put qgreylistrbl instead of rblsmtpd in the command line for starting qmail-smtpd.

Performance

qgreylistrbl is a Perl script. Expect some CPU usage. If you run a QMAILQUEUE-patched version of qmail-smtpd and spamassassin, the load will decrease extensive, because most connection attempts do not cause a mail delivery. With perl > 5.6.1 you can precompile the source code with perlcc.

Installation:

Just copy the perl script wherever you want and edit the start script for qmail-smtpd. qgreylistrbl is a simple replacement for rblsmtpd from D.J. Bernstein and can be used the same way.

Create the greylist IP folder:

# mkdir /var/qmail/qgreylistrbl
# chown qmaild /var/qmail/qgreylistrbl

Adjust User

If you need to install the perl module Mail:RBL, just do the following:
From the root prompt on your server, invoke the CPAN shell:

# perl -MCPAN -e shell

Once the Perl interpreter has loaded (and been configured), you can install modules by issuing the command install MODULENAME.

The first thing you should do is upgrade your CPAN:

cpan> install Bundle::CPAN

Once its done (it will take a while, just enter all questions), type:

cpan> reload cpan

Now, enter the following command to retrieve all of the required modules:

cpan> install Mail::RBL

Then you can be shure everything is installed to correct locations.

Configuration:

At the beginnung of the script you have to adjust a few variables. See script for more details. Important are hostname, working directory, some paths and RBL services. You have to add a crontab entry as follows:

*/20 * * * * vpopmail /var/qmail/bin/qgreylist_cleanup.pl

Adjust user, path and time before.
Dont forget so set up logging facility in /etc/syslog.conf

PHPrbl is a quick and easy tool that keeps clients using open proxies away from your site in order to reduce referrer spam.
Ever had those annoying referrer spammers ruin your websites statistics? If you run a big website, or a weblog, you must be getting fed up with this blasted referrer spam.
Youre not alone, I have this problem as well and got fed up with the whole thing. After weeks of playing with the idea of blocking referrer spammers using rewrite rules, I got fed up wit the high amount of energy it would demand of me just to block IP addresses that seemed to be open proxies anyway.
Enhancements:
- Streamlined the code based on input given by Steven Lynn. Fewer queries are now used to do the same thing. Thanks!
- New feature: keywords checking; referrers are now matched to keywords given by the site admin. If a match occurs, the client will be blocked. (For myself this feature has already proven to be very, very effective)
- First start of an admin area for PHPrbl, for now, only the ability to add and removed keywords is present. Whitelisting and local IP blocklist management will be added soon.

Ultratron is an arcade game where you have to destroy the four evil robots of the Apocalypse!
The last human has been slain by evil killer robots. You are the one remaining humanoid battle droid. Your mission is to avenge the human race, and destroy the four bots of the Apocalypse - Ieiunitas, Bellum, Lues and Letum!
Power up your droid with ever more powerful weaponry as you blast your way through the levels, avoiding Chasers, Turrets, Spawners, Minelayers, bombs, and bullets!
Main features:
- 70+ different robots to destroy
- 40+ levels of frantic shooter action
- 4 giant boss robots
- 10 powerups
- Bonus stages
- Online hiscore table

The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems.

What we are trying to do is to create a framework for testing, and a core set of tests that all may download and use to probe specific elements of systems performance.

Moreover, the source to these tests are available under GPL, and are hosted on Bioinformatics.org and Scalable Informatics LLC The idea is to enable end users, consumers, systems developers, and others to easily build and use meaningful tests for measurement and tuning reasons.

Joe Landman from Scalable Informatics LLC conceived the idea and wrote the original codes. We are looking for additional benchmark code suggestions, tests, data sets, etc.

Current baseline tests are several NCBI BLAST runs, several HMMer runs, and a variety of others. We plan to include ClustalW, X!Tandem, various chemistry, dynamics, and related tests, as well as several others.

Tests such as LINPACK or HPL simply do not provide meaningful performance indicators or predictive models for high performance informatics. Unfortunately, nor do a number of more recent and focused tests.

This is a problem as LINPACK and HPL specifically test the performance on various matrix operations, where you have effectively regular memory access patterns, and specific mathematical operations.

These codes are most useful for comparison to codes with heavy floating point operations, and interleaved memory traffic. These codes were not designed for comprehensive systems benchmarking, where disk I/O, memory latency, and other factors all contribute to the performance issues.

The best tests are the ones that are most similar to the codes you will run on the machine. The tests themselves should be reasonable approximations to a real execution of your code, using real data. You may need to pare it back in order to get realistic run times.

You should have a reasonable subset of data sizes. A single test does not tell you how your system scales, and one of the reasons for the existance of this test is specifically to allow you to test the performance while you increase various aspects of the workload.

You rarely get a quiescent system in a cluster, so we would recommend that you try to run in as realistic an operating environment as possible. A baseline in a quiescent system is fine, but it may set your expectations unreasonably.
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Volume.app is a small graphical software utility enabling quick and convenient control of a computers audio volume level. Volume.app is intended for use on Linux/Unix systems in conjunction with an X window manager that supports dockable applications ("dockapps") such as AfterStep, BlackBox, or Window Maker.

It is a refinement of an idea that first appeared in Timecops WMix: a user interface comprising a "knob" that can be interactively "turned" by clicking and dragging the mouse. I found this approach quite appealing, both from an aesthetic viewpoint, and (more importantly) from a user-interface perspective.

A handful of other dockapp volume control programs are out there, and I have tried many of them. An interface element present in most of these is some form of "slider" as the primary means of adjusting the volume. (A fictitious example may be seen at right). To my dismay, with this kind of interface, volume adjustments tended to be large and abrupt. Because the slider was so small, raising or lowering the volume "just a bit" required extremely careful control of the mouse-- a slip of the hand had the potential to spike the volume to full blast. (I have a set of Altec-Lansing ACS48 speakers which make this a rather unpleasant experience). This approach left much to be desired.

I longed for an alternative, and upon playing with WMix (pictured at left) I had found it. The knob was genius in that it provided a means of graphically adjusting the volume, as a slider would, without tying itself directly to the motion of the mouse. The basic mode of usage is identical: you click on the thing and drag the mouse up or down. However, with the knob, the range of motion need not be confined to the postage-stamp-sized area of the dockapp. The mouse travel needed to cover the entire range of volume settings can be made longer, on the order of the full height of the screen-- almost like a much larger, easier-to-use slider. No longer were precise movements needed to make volume adjustments!

Still, I found WMixs interface to be a bit busy (never was a fan of tiny little buttons) and the all-important knob was yet a rather small target to find with the mouse. So, I grabbed a copy of the WMix source code, and rebuilt it into a dockapp that had a much larger knob as its sole interface element. I dubbed it Volume.app, and have placed it here for the benefit of everyone.