Free 1.5.1 software for linux

This program places the required number of sodium ions around a system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex).

The ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy:

Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|

All the constants are dropped out from this formula, resulting in some weird energy units; that doesnt matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations.

The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage.

It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.

T-BEAR is the Transient Bluetooth Environment security AuditoR. It includes an ncurses-based BT scanner, a Bluetooth DoS proof-of-concept, and a "hidden" BDADDR hunter similar to Redfang 2.5.
Other tools based on gnuradio are being developed, including a BT "sniffer".
Enhancements:
- Minor feature enhancements

R2cl compiler is a minimal, proof of concept translator from the R or S language into Common Lisp.

An increase in speed of over 1000 times can then be achieved using the free CMU Common Lisp native code compiler on the resulting code, making it comparable to FORTRAN, Ada or C.

Installation:

To install you need first to install cmucl (the CMU Common Lisp) and R. Both come with most Linux distributions by default but you must select them for installation. I think most recent (after 2000) versions will work. I have R 1.5.1 and cmucl x86-linux 3.0.8 18c+ running on Debian 3.0 (woody). You must be running the bash shell (which is the default) and have gnu make on your system (which you normally have).

Just untar the distribution archive:

tar xvzf R2cl-0.1.tgz

It will create the directory R2cl. Type:

cd R2cl
make

and watch translation, compilation and duration of execution of benchmarks. Thats all, except if you want to have a look at the code.

R is a reimplementation of the S language for statistical processing. It is a free project, see r-project.org. R is a highly expressive matrix language (it makes extensive use of matrix and vector operators) with a huge library of statistical functions. However, expressivity requires a dynamic execution engine based on an infinite memory model which is slow.

It also requires that expressions and function can be constructed by a program or introduced by an operator at runtime thus enforcing the an interpreted approach. This makes strighforward implementations of it slow. For programs that might have an equivalent in FORTRAN, that FORTRAN equivalent would be over 1000 times faster.

Lisp is a language with the same execution model, except the that it is even more general, and include extensive macro and object oriented feature. There are may flavors, but the main currents are Scheme (which is reductionist, favoring simplicity) and Common Lisp (the ISO standard which is extensive and highly concerned with efficient compilation).

None of these languages would be easy to fully translate, say, in C. To have the complete language you need, at least in part, to have the intepreting engine and the infinite memory machine intimately combined with the generated code.
However, there is no reason for pieces of code which make no use of the generality (such as source code generation and execution at runtime) not to be compilable to code as fast as FORTRAN. In practice, this is a huge task. Nevertheless, it was achieved in a free implementation, for example in CMU CommonLisp, as I was delighted to learn when trying these benchmarks.

The semantics of R is a subset of the semantics of Scheme. It also includes, of course, a wealth of data types suitable for statistics. The semantics (expressive mechanisms) of CommonLisp are probably a superset of Scheme. This means that R is easy to express in Scheme (actually the engine of the free implementation is a Scheme engine) and perhaps easy to translate in CommonLisp. This later is interesting because of the availability of the efficient compiler.

So I arrived at this toy project, to check if such a route for the efficient compilation of R is possible.

Many R applications dont need speed. You can describe the job you need done so quickly that you rarely mind to wait a couple of seconds for the system to do it. However, there are also whole classes of applications where speed is necessary and if a complete porting of R on CommonLisp (really big project) would be done they would all become feasible for R users like myself.

VCalendar is an open source Web calendar application with related tools, for posting and maintaining events and schedules online, in calendar format.
VCalendar project is an excellent and free solution for use by online Web communities and any commercial and non-commercial organizations. Unlike any other online calendars, VCalendar comes with source code in multiple programming languages: PHP, ASP and ASP.NET (C# and VB.NET); with potential for adding more technologies in the future.
Main features:
- Localization features, with initial Internationalization in English and Russian, with language selectable by end-users
- Dynamic CCS (stylesheet) styles, selectable by end-users
- Annual, monthly, weekly and daily calendar views
- Multiple categories for classifying calendar events
- Recurring and all-day events
- Role-based user permissions and calendar configuration
Enhancements:
- Fixed the bug reported on SourceForge Forum: 3771522: Unable to select Month or the Year

SLAMPPLite is a linux live CD that will turn your personal computer to a simple home server.
What makes it different is that SLAMPPLite has smaller size that will fit into a 256 MB compact disk or usb stick. It contains only essential server applications like Apache, MySQL, ProFTPD, BIND, DHCPD, SSH and mail server.
Several programming languages such as PHP, Perl and Python and other tools to support your web development work are also included.
To keep SLAMPPLite slim and make it easy to update the applications, SLAMPPLite uses server suite provided by XAMPP.
SLAMPPLite is compiled intended to be your showcase box. So, when you have something to show to your (potential) users or clients, just put your web applications on SLAMPPLite and you will have an instant mobile portfolio.
Therefore I advise you not to use SLAMPPLite for production purpose, just use the standard SLAMPP instead. Although through some tweaks here and there, SLAMPPLite is also ready for that. Please remember, SLAMPPLite comes with ABSOLUTELY NO WARRANTY. It is provided as AS IS product. Please use it at your own risk.
Main features:
- Linux kernel: 2.6.16
- Desktop: Xfce 4.2.2
- Web, FTP and database servers: XAMPP 1.5.1
- Other servers: BIND, DHCP, Sendmail. Dovecot, SSH
- Programming:
- Languages: PHP 4.4.1/5.0.5, Perl 5.8.7, Python 2.4.1
- Editor: Bluefish 1.0.4
- Office: Xpdf
- Graphics: Xpaint
- Multimedia: Beep Media Player, BashBurn
- Network: Nmap, Putty, BitTorrent 4.2.1 (tracker/client), FTP client, Firestarter firewall
- Internet: Mozilla Firefox 1.5, Sylpheed 2.0.4, Gaim 1.5.0
- Package management: pkgtool, slapt-get/gslapt
- Antivirus: ClamAV 0.87.1, FetCav (GUI)
- Utilities: GParted, EmelFM2, Dufie, htop, rkhunter, Qemu, backup system and hard disk installation scripts
- Complete list of packages can be found over here, SLitePackages.
Enhancements:
- Updated and upgraded existing applications included in previous SLAMPPLite Live CD
- Powered by XAMPP 1.5.1 and now it exists as module (xampp_1_5_1.mo)
- Based on Slackware current
- Used linux kernel 2.6.16
- Compiled with Linux Live scripts 5.4.1
- Added NASLite File Servers applications of Server Elements for SMB, FTP and NFS. They can be found under /tools directory of CD.
- Added Abiword 2.4.1
- Added Freerock GNOME support via slapt-get
- New hard disk installation program provided by Nonux
- Web documents installation scripts is now separated from XAMPP boot scripts. You can execute it from Xfce menu, or manually: # bash /opt/slampp/install.sh
- Fixed fstab

SDTS++ is a C++ toolkit that programmers can use to write applications that can read or write SDTS datasets.
Application developers can use SDTS++ library classes to work with the logical structure of these datasets without having to worry about the physical details of each dataset.
What compilers does it work with?
SDTS++ is known to work with:
- GNU g++ 2.8.x and 2.95.x
- egcs 1.x.y
- Microsoft Visual C++ 6.0 (Apply latest service pack!)

libgmail project is a pure Python binding to provide access to Googles Gmail web-mail service.
Please note: Always download and test the CVS version of libgmail if you are having problems. The most recent packaged version no longer works correctly. The current development status means critical errors caused by changes at Gmail will be corrected as soon as possible in CVS, if the author is notified about the issue.
Archive Gmail messages to mbox format
The library currently ships with one demonstration utility to archive messages from an Gmail account into mbox files, suitable for importing into a local email client.
Use your Gmail account as a SMTP server
The library now includes a demonstration utility gmailsmtp.py that sets up a SMTP proxy on port 8025 of your computer to enable you to use a standard mail client (e.g. Mozilla, Mail.app) to send messages. (Attachments are now supported.)
Use your Gmail account as a POP server
The library now includes a demonstration utility gmailpopd.py that sets up a POP3 proxy on port 8110 of your computer to enable you to use a standard mail client (e.g. Mozilla, Mail.app) to retrieve messages.
Use your Gmail account as a FTP server!
The included demonstration gmailftpd.py sets up a download-only FTP proxy on port 8021 of your computer to enable you to use a standard ftp client to retrieve message attachments that have the label ftp.
Enhancements:
- Minor bugfix -- before, if you logged in with an incorrect password, the program would exit poorly instead of throwing the appropriate exception.