Optimal production of biological documentation: the JAM format

The current environment for providing documentation for users in molecular biology frequently requires written information for both printed and electronic media. The JAM (Just Another Metafile) Format requires that only a single file of text is written. This is, then, processed by the jam program which converts this text to a document set which is suitable for on-line documentation in the hypertext mark-up language (HTML) of the World Wide Web system. For printed output, the jam program can produce either text in wordprocessor-ready Rich Text Format (RTF), or source code for the LaTEX typesetting system. The latter allows for professional text layout and can generate, amongst other formats, postscript files to be printed on a variety of device

Hierarchical Access System for Sequence Libraries in Europe (HASSLE): a tool to access sequence databases remotely

Sequence databases in biology are growing exponentially. Not only are large sites needed to keep the data, but the number of customers is continuously increasing. Network access plays a key role in utilizing remote resources. However, both synchronous and asynchronous access require tools that are currently non-standard in molecular biology computing. Additionally, information discovery of today frequently focuses on centers rather a hierarchically interconnected facilities. HASSLE (Hierarchical Access System for Sequence Libraries in Europe) is an implementation of an application-independent, user-transparent access tool in molecular biology. It features tools for both clients and information providers to permit accounting and/or prioritization on various levels. HASSLE focuses on the network aspect of the molecular biology computing and assumes that it is possible to have database applications as remote ‘services' (programs, program packages or utilities) which can be started by a simple command script after a suitable feed of datafiles. The current system provides these services for searching with programs like FASTA or BLAST which are compiled as obtained from vendors or server

A compression mechanism for sequence databases to improve the efficiency of conventional tools

This paper describes a method to compress molecular biology databases that are characterized by an increasing proportion of data derived from genome projects. The performance of our tool has been tested on various data files of the EMBL nucleotide sequence database. The best compression ratios were achieved on EST (Expressed Sequence Tags) data, typically derived from large-scale sequence projects. The compression of sequence database updates was tested in combination with the common Unix compression program ‘compress'. Our tool improved the efficiency of ‘compress' on average by 16

Simplified user poll and experience report language (SUPER): implementation and application

Biological computing is generally organized as standalone implementation on a PC-type computer or on a central facility (e.g. a university computer center). Services provided by central facilities need to be tailored to the user community. Unless very work-intensive individual contacts are used, the feedback must be collected with generalized tools, such as questionnaires distributed in the form of a newslettter. We have developed a method to have such polls automated and tailored, as well as having multiple-choice questions combined with branching after fundamental questions. As the evaluation of the results needs to know the questions asked, we have also included a method to process the answers and give detailed tables on the answers. SUPER was applied in a poll to query the academic usership in Switzerland on the usage of molecular biology database

FastAlert-an automatic search system to alert about new entries in biological sequence databanks

This paper describes a new tool enabling awareness of new sequence databank entries of interest. The Fast Alert system relieves the researcher from the burden of repeating FASTA searches in order to keep up with the rapidly growing amount of information found in biological sequence databanks. The query sequence can be submitted from any computer connected to the Internet. Upon registration, the databank, including the updates, is scanned at periodic intervals with the sequence provided. The results, so-called FastAlert reports, are delivered via electronic mail. The reports contain the FASTA best-scores list and the similarity statistics for each entry liste

Simplified user poll and experience report language (SUPER): implementation and application

Biological computing is generally organized as standalone implementation on a PC-type computer or on a central facility (e.g. a university computer center). Services provided by central facilities need to be tailored to the user community. Unless very work-intensive individual contacts are used, the feedback must be collected with generalized tools, such as questionnaires distributed in the form of a newslettter. We have developed a method to have such polls automated and tailored, as well as having multiple-choice questions combined with branching after fundamental questions. As the evaluation of the results needs to know the questions asked, we have also included a method to process the answers and give detailed tables on the answers. SUPER was applied in a poll to query the academic usership in Switzerland on the usage of molecular biology database