ICOT FREE-SOFTWARE News Letter No.6

                                     14, October, 1993

[Table of Contents]

• Newly released ICOT Free Software
• User's Group
• About Common ESP
• Contacts

[Newly released ICOT Free Software]

1) Newly Released Software

  The following lists the new programs:

Symbol Processing: 3
- - ----------------------------------------------------------------
72  Portable KL1 processing system: experimental version
    /ifs/symbolic-proc/unix/pkl1.tar.Z             130871 bytes

73  Process oriented programming language AYA
    /ifs/symbolic-proc/pimos/aya.tar.Z             235617 bytes

74  KL1 Load Distribution Library
    /ifs/symbolic-proc/unix/ldlib.tar.Z            123055 bytes


Applications programs of parallel logic programming: 3
- - ----------------------------------------------------------------
75  Multiple Sequence Alignment by Parallel Iterative Aligner
    /ifs/exper-apps/pimos/multialign.tar.Z         178138 bytes

76  Intelligent Refiner for Multiple Sequence Alignment
    /ifs/exper-apps/pimos/editalign.tar.Z          710383 bytes

77  Protein Structure Visualization system: Protein View
    /ifs/exper-apps/unix/proview.tar.Z             997633 bytes  

2) Detailed Description

1. Portable KL1 processing system: experimental version

The first and experimental version of the KLIC system for investigating execution method of KL1 programs on UNIX systems has been released.

KLIC translates KL1 programs into equivalent C programs, which are compiled and linked with the KLIC runtime library to obtain an executable. This version runs only sequentially, but parallel versions will be available eventually.

The compiler of this version is written in Prolog. An Edinburgh Prolog compatible and a C language system are needed for to use it. With Prolog and C language systems, the KLIC system can run on any computer, including personal computers. Future releases of the compiler will be written in KL1 make the Prolog system unnecessary.

Since this version is developed to investigate execution method of KL1 programs on UNIX systems, there are no convenient facilities such as debugger, etc. A version of KLIC with these facilities will be released soon.

2. Process oriented programming language AYA

AYA is designed upon KL1. Using AYA, it is easier to write and read parallel logic programs than it would be when using KL1. Furthermore, it is easy to avoid and fix AYA programs bugs.

Message communications between processes can be expressed directly in AYA programs. Processes can have several states. Input and output process modes are also introduced. Variables and streams for communication between processes can be terminated automatically.

3. KL1 Load Distribution Library

The load distribution library is a set of utilities that implement typical load distribution schemes such as network generation, process mapping, and dynamic load distribution for KL1 programming.

The library provides templates for typical distribution schemes. A parallel program for solving a given problem is created by linking this library with problem-specific code written by the user.

4. Multiple sequence alignment by Parallel Iterative Aligner

This program solves multiple alignment problems that align similar parts of protein sequences. The parallel iterative aligner, a method of repeating partiall improvement by using dynamic programming, is implemented.

Put concretely, possible partial improvement is done on each processor in parallel, with the best result being selected. This is a sort of hill-climbing method, the program being written in KL1. This program solves large scale multiple alignment problems with high quality on PIM. For example, aligning 20 sequences,each of which consists of 80 characters requires about 10 minutes on PIM using 256 processors.

The result of this program has a confidence high enough to allow the investigation of biological considerations. Analyzing the behavior of this program will provide you with valuable knowledge on parallel information processing and parallel load distribution.

5. Intelligent Refiner for Multiple Sequence Alignment

This program refines a protein sequence aligned by Multiple Sequence Alignment with biological knowledge. This program has an interface to obtain knowledge such as the plan a biologist uses for refining protein sequences.

This program is providfed with automatic aligner with constraints, that acts on a part of protein sequences designated by the user, using the mouse interface. The automatic aligner with constraints aligns protein sequences, keeping part of the sequences fixed by user. This program is written in C with Xlib and OSF/Motif, making it easy for users to handle.

The alignment of part of protein sequence is processed by KL1 program, with the result of the alignment appearing on the display. This program has an alignment editor that can insert and delete gaps, as well as search for a motif by means of the mouse interface.

6. Protein Structure Visualization System: Protein View

This system displays the three-dimensional structure of a protein on a graphical work station. This system consists of tow parts, Pro-View and 3D-View.

Pro-View reads protein data from PDB(Protein Data Bank) and generates graphical object description language 3D-talk. 3D-View is a three-dimensional general purpose visualization tool that interprets 3D-Talk.

3D-View can visualize not only protein structures, but also robot structures and flight simulation. It also lets you animate these objects.

3D-Talk is a object-oriented language. It is easy for beginners to understand because its grammar is similar to that of English. Pro-View is a tool for analyzing protein structures. It features a Pro-Talk, an extension of 3D-Talk. This system provides a powerful means of visualizing processes such as protein folding simulation.

The ICOT Free Software Catalog-II has recently been published. Its contents explain these new programs that have released as ICOT Free Software. Anyone wishing to obtain this catalog is invited to contact the IFS desk via e-mail, mail or fax at the address at the end of this newsletter.

[User's Group]

We hope to feature some of your proposals in the next issue of the newsletter. Reactions to your proposals shall also be forwarded to you.

Revised programs can be stored on the FTP server at ICOT, if you feel that your revision would be useful for other users.

[About Common ESP]

        Research Management Department
        AI Language Research Institute, Ltd.

        c/o Computer & Information Systems Laboratory
        Mitsubishi Electric Corporation
        1-1, Ofuna 5-chome, Kamakura
        Kanagawa 247 Japan

        e-mail: cesp-request@air.co.jp
        FAX:    +81-467-48-4847

[Contacts]

ifs@icot.or.jp

by e-mail. If you receive a paper edition of this newsletter, let us know your e-mail address and we shall send you the electronic edition. If you do not have an e-mail facility, contact the address below.

All available IFS is listed in "ICOT Free Software Catalog" and "ICOT Free Software Catalogue II" . If you do not have a copy of either catalog, supply the IFS-desk with your postal address and we shall arrange to send a copy to you.

If any of your colleagues or acquaintances are interested in IFS, let us know their name and both their e-mail and postal addresses, and we shall arrange to send them both the newsletter and catalog.

        ICOT Free Software desk

        Institute for New Generation Computer Technology
        21st Floor, Mita Kokusai Bldg.
        4-28, Mita 1-chome
        Minato-ku, Tokyo 108
        Japan

        FAX:   +81-3-3456-1618