JaMBW 1.1

Welcome to the first public release of JaMBW, the Java based Molecular Biologist's Workbench ideated, coordinated by Luca I.G.TOLDO User Consultant at the European Molecular Biology Laboratory of Heidelberg, and realized thanks to the coding efforts of :Rob Beynon, Eugen Buehler, Ramu Chenna, Andrey Grigoriev, James Knight, Elizabeth Odekirk, PHD Computer Consultant Ltd., Luca I.G. Toldo and Dirk Walther.

What is beneath this page:

***NOTE FROM BIOINFORMATICS.ORG: JaMBW is not an open-source project but is provided here as a free online tool. The license doesn't permit decompiling, but Luca Ida Giovanni Toldo (the author) has communicated the following:

All the source code could be easily generated automatically with [DJ Java Decompiler], and I would have no objection of making that source opensource: it could even bring "more life" to the project as well as facilitate some didactic use (e.g. see how given algorithms work).

If an open-source version of JaMBW is not provided to the community, this software will not be permanently hosted at Bioinformatics.Org.


The programs and documentation that you will find hereby enclosed had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use. The latter includes, therefore, point-and-click, drag-and-drop, plug-and-play. Most of these requirements are met by the use of Java programming language conformant to the JDK1.02 specifications. To the user of these resources, however, the implementation details are of null interest. And thus JaMBW, simple to use, "runs" everywhere, is simple to install and to get rid of, is free.

What is not

JaMBW in its current release is certainly *NOT* a complete molecular biology software package. It might become, and if it will be so depends very much from your support and feedback.

Tested on

JaMBW is designed to be able to provide its services regardless to the kind of computer, operating system, and software the user has available. The only foundation on which it relies is a Java Virtual Machine (JVM). Exists JVM for almost any kind of computer and operating system, and in the near future it will probably be included as component of each operating system. At the time of this release, however, JVM is not yet included automatically in each computer but is rather simple to do that. Infact, exist several programs that include the JVM into their own capabilities, and the resources here provided had been indeed tested with the following combinations of hardware and software. The following list, however, is not restrictive and it might be well happen that your setup although not included in the following list indeed works. Would not be the case, please inform me.
HardwareOperating SystemJVM
Apple PowerPC7.5.3Sun JDK 1.02
Netscape Navigator 3.01
Netscape Communicator 4.0b2
Symantec Caffeine
Metrowerks gold 9.0
Apple MRJ 1.0b1
Microsoft Internet Explorer 3.0
IBM CompatibleWindows 95Netscape 3.01
Netscape Communicator 4.0b2
Microsoft Internet Explorer 3.0
Windows NTNetscape 3.01
Netscape Communicator 4.0b2
Microsoft Internet Explorer 3.0
Linux 2.0Netscape 3.0
Microsoft Internet Explorer 3.0
Silicon GraphicsIrix 5.3Netscape 3.01
Digital Equipment CorporationUltrixNetscape 3.01
UltraSparc 1Sun OS 5.4HotJava
Netscape 3.0


I have performed thorough debugging and checked each of the operations of all the programs and contents of the information and services provided you by JaMBW. However, errors are human and therefore I request you to notify any error / malfunctioning / imperfection that you could discover. This implies that although the software is provided as-is (and thus I assume no responsibility on the consequences of its use even if done appropriately), the best will be done in order to include your comments / reports in the online and future versions of it.

The search tool is provided by using the HelpIndex software developed by PH.D.Consultants.ltd.. Hereafter follows the text they present on their front page for using this software.

Small Print

HelpIndex, HlpIndex, HlpIndices, GridBagForm, GBFcomponent, HelpIndexFrame, HelpIndexForm, PHDUtils, MakeHelpIndex, ParseHTML and HTMLuser are Copyright © 1996 PHD Computer Consultants Ltd.

HelpIndex and MakeHelpIndex are shareware.
Please try for free for 30 days. There is no lock-out mechanism after this period.
After 30 days, please pay for registration or remove HelpIndex from your system.

To register please send us your details and pay us UK 25 (about US$35) if you are a small organisation or UK 200 (about US$300) for larger commercial use. Please let us know if you want a formal invoice.
The UK prices include VAT at 17.5%. If you are in the European Union and are VAT registered then please tell us your VAT number, and we will bill you without any VAT. Sales outside the EU have no sales tax.
Currently we cannot handle on-line transactions safely, so please send payment details directly to PHD:
PHD Computer Consultants Ltd

Registered in England: 2982041
VAT No: GB 553-4462-43

27 Rippingham Road, Withington, Manchester M20 3FX
Telephone: (+44) (0) 161 445 1650
Fax: (+44) (0) 161 445 4707

Email: good-tech@mcr1.poptel.org.uk

Web site: http://www.poptel.org.uk/phdcc
FTP site: ftp://ftp.poptel.org.uk/pub/phdcc

Please send cheques in pounds sterling or give us your credit card details (type, number, name, address and expiry date). We will confirm credit card details by telephone or email. Credit card deductions will be made in pounds sterling and converted to your local currency by the time they appear on your bill. If you are able to transfer payment directly into our bank account, then email us and we will reply with our bank details.

You can have a full refund if you have a legitimate problem with the software. However we do not envisage this option being used often, as you will have had a chance to try before you buy.

Registering HelpIndex covers the current version and any releases in the coming year. Currently registered users do not receive a physical copy of HelpIndex. However you will receive priority technical support.

Contact us if you would like to resell HelpIndex or any other PHD product.

We will put you on our mailing list to keep you informed of future developments.
If you like, please let us know what URL you are using.
At the very least, please email us to let us know that you are using HelpIndex, and give us feedback.

We may be able to offer an outlet with support in USA soon.

PHD Computer Consultants Ltd makes no representations or warranties about the suitability of the software, either express or implied, including but not limited to the implied warranties of merchantability, fitness for a particular purpose, or non-infringement PHD Computer Consultants Ltd shall not be liable for any damages suffered by user as a result of using, modifying or distributing the software or its derivatives.

JaMBW Editor:Luca I.G. TOLDO, Edition date: 28 February 1997