DIGICALC: a restriction fragment analysis program.

DIGICALC is a program designed to aid in the acquisition, storage, and analysis of nucleic acid restriction fragment data. The chief considerations during program design were (i) ease of use for people with varying degrees of computer experience, (ii) minimal hardware requirements (e.g. an IBM PC), (iii) portability and ease of modification, and (iv) improved functionality in sizing and comparing restriction fragments over manual methods. The program accepts manual or digitizer input of nucleic acid fragment mobility, calculates the fragments' sizes, and provides the means to search the fragment database and to produce charts of fragment sizes.     

Memory for events and their spatial context: models and experiments

The computational role of the hippocampus in memory has been characterized as: (i) an index to disparate neocortical storage sites; (ii) a time-limited store supporting neocortical long-term memory; and (iii) a content-addressable associative memory. These ideas are reviewed and related to several general aspects of episodic memory, including the differences between episodic, recognition and semantic memory, and whether hippocampal lesions differentially affect recent or remote memories. Some outstanding questions remain, such as: what characterizes episodic retrieval as opposed to other forms of read-out from memory; what triggers the storage of an event memory; and what are the neural mechanisms involved? To address these questions a neural-level model of the medial temporal and parietal roles in retrieval of the spatial context of an event is presented. This model combines the idea that retrieval of the rich context of real-life events is a central characteristic of episodic memory, and the idea that medial temporal allocentric representations are used in long-term storage while parietal egocentric representations are used to imagine, manipulate and re-experience the products of retrieval. The model is consistent with the known neural representation of spatial information in the brain, and provides an explanation for the involvement of Papez''s circuit in both the representation of heading direction and in the recollection of episodic information. Two experiments relating to the model are briefly described. A functional neuroimaging study of memory for the spatial context of life-like events in virtual reality provides support for the model''s functional localization. A neuropsychological experiment suggests that the hippocampus does store an allocentric representation of spatial locations.     

Interactive computer supported tumor registry in the state of Rhode Island.

A new interactive computerized tumor registry has been established for the state of Rhode Island. The registry is implemented with new data base software which features a pagination scheme with rapid retrieval of non-coded variable data. The types of data stored are discussed as well as the computer system and methods of data entry storage and retrieval.     

Revealing biological information using data structuring and automated learning

The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents.     

Computerization of data capture for mouse skin painting studies

An interactive data input, storage, retrieval and treatment system for mouse skin painting studies is described. The system was implemented on a Hewlett-Packard (HP)1000-F computer under RTE IVB operating system using FORTRAN IV. The program's simple design means that it can be run easily by unskilled personnel.     

A discrete model of bacterial metabolism

This paper describes a computer model of the intermediary metabolismof bacteria during steady-state growth and during adaptations,e g. to new carbon sources. Metabolic regulation is representedas a process of optimisation, in which the trend is towardsimproved metabolic performance. The model uses linear programmingtechniques for the optimisation The implementation falls intofour phases: (i) assembly of model parameters; (ii) calculations;(iii) storage of solutions and (iv) projection of solutions.The use of a commercial database and a commercial spreadsheethas proved to be of great assistance in the first and thirdphases. A metabolic map format, with the optional addition ofconversion values, names of enzymes or co-factors has been usedto project the results in a form convenient for inspection. Received on August 22, 1985; accepted on January 3, 1985     

Metric-space indexes as a basis for scalable biological databases

Biochemical databases will be best served by the development of new specialized database management systems whose storage managers are based on metric-space indexing techniques and the development a database query languages that embody semantics derived from biochemical models of similarity and evolution. Important biochemical data types cannot be effectively mapped to low dimensional coordinate systems on which O(log n) indexing methods rely. It is clear from an abundance of bioinformatic discoveries that biochemical data is not random and exhibits interesting structure with respect to clustering. Metric-space indexing exploits a data set's intrinsic clustering to speed the execution of similarity queries, even when the data cannot be mapped to a coordinate system. Database management systems that seamlessly integrate semantically rich query languages with a metric-storage and retrieval mechanism will allow biologists to simply and concisely develop informatic studies that have traditionally been large and labor intensive.     

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases

MOTIVATION: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. RESULTS: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. AVAILABILITY: http://www.molgenis.nl     

The RAINFOR database: monitoring forest biomass and dynamics

Problem: Data from over 100 permanent sample plots which have been studied for 10–20 years need a suitable system for storage which allows simple data manipulation and retrieval for analysis. Methods: A relational database linking tree records, taxonomic nomenclature and corresponding environmental data has been built in MS Access as part of the RAINFOR project. Conclusion: The database allows flexible and long‐term use of a large amount of data: more than 100 tree plots across Amazonia, incorporating over 80 000 records of individual trees and over 300 000 total records of tree diameter measurements from successive censuses. The database is designed to enable linkages to existing soil, floristic or plant‐trait databases. This database will be a useful tool for exploring the impact of environmental factors on forest structure and dynamics at local to continental scales, and long term changes in forest ecology. As an early example of its potential, we explore the impact of different methodological assumptions on estimates of tropical forest biomass and carbon storage.     

A computer system automatic analysis of vectorcardiograms.

This computer system performs the analysis of orthogonal electrocardiograms for vectorcardiographic (VCG) display and classification. The data acquisition can be performed 'on-line' with the complete analysis in 'real-time', or off-line by processing a magnetic tape. The original computational methods for beat averaging and wave recognition are described. Some features, such as the quality of the visual display of the VCG traces, the availability of a measurement matrix allowing the quantitative analysis of the VCG and the use of a data bank for storage, retrieval and statistical studies make this system very efficient for clinical purposes, introducing the concept of 'Computer Assisted Vectorcardiography'.     

A Grid-based solution for management and analysis of microarrays in distributed experiments

Several systems have been presented in the last years in order to manage the complexity of large microarray experiments. Although good results have been achieved, most systems tend to lack in one or more fields. A Grid based approach may provide a shared, standardized and reliable solution for storage and analysis of biological data, in order to maximize the results of experimental efforts. A Grid framework has been therefore adopted due to the necessity of remotely accessing large amounts of distributed data as well as to scale computational performances for terabyte datasets. Two different biological studies have been planned in order to highlight the benefits that can emerge from our Grid based platform. The described environment relies on storage services and computational services provided by the gLite Grid middleware. The Grid environment is also able to exploit the added value of metadata in order to let users better classify and search experiments. A state-of-art Grid portal has been implemented in order to hide the complexity of framework from end users and to make them able to easily access available services and data. The functional architecture of the portal is described. As a first test of the system performances, a gene expression analysis has been performed on a dataset of Affymetrix GeneChip Rat Expression Array RAE230A, from the ArrayExpress database. The sequence of analysis includes three steps: (i) group opening and image set uploading, (ii) normalization, and (iii) model based gene expression (based on PM/MM difference model). Two different Linux versions (sequential and parallel) of the dChip software have been developed to implement the analysis and have been tested on a cluster. From results, it emerges that the parallelization of the analysis process and the execution of parallel jobs on distributed computational resources actually improve the performances. Moreover, the Grid environment have been tested both against the possibility of uploading and accessing distributed datasets through the Grid middleware and against its ability in managing the execution of jobs on distributed computational resources. Results from the Grid test will be discussed in a further paper.     

A database of mutants and effects of site-directed mutagenesis experiments on G protein-coupled receptors

A database system and computer programs for storage and retrieval of information about guanine nucleotide-binding protein (G protein) -coupled receptor mutants and associated biological effects have been developed. Mutation data on the receptors were collected from the literature and a database of mutants and effects of mutations was developed. The G protein-coupled receptor, family A, point mutation database (GRAP) provides detailed information on ligand-binding and signal transduction properties of more than 2130 receptor mutants. The amino acid sequences of receptors for which mutation experiments have been reported were aligned, and from this alignment mutation data may be retrieved. Alternatively, a search form allowing detailed specification of which mutants to retrieve may be used, for example, to search for specific amino acid substitutions, substitutions in specific protein domains or reported biological effects. Furthermore, ligand and bibliographic oriented queries may be performed. GRAP is available on the Internet (URL: http://www-grap.fagmed.uit.no/GRAP/homepage.html ) using the World-Wide Web system. © 1996 Wiley-Liss, Inc.     

IRAP — A system for the retrieval and analysis of orthopaedic implant data

An interactive computer system for the storage, retrieval and analysis of standardized clinical and material characterization data associated with orthopaedic implants is described. The system consists basically of four independent modules. The essence of the system centers on the cross-referencing capabilities which are virtually unlimited. The system has been designed for use by non-computer trained personnel.     

Method for Coding Data on Protozoan Strains for Computers

SYNOPSIS. Traditionally, observations on the nature of protozoa have been published in periodicals or books, or remain buried in research notebooks. The retrieval and processing of information on a particular species or strain are dependent solely upon individual investigators. Although various modern methods have been applied to the study of protozoa, no attempt has been made to develop a system with which information on protozoan strains can be stored, retrieved easily, and processed for various analyses by computer technology. Based upon an existing system for encoding data on bacterial strains, a complementary system applicable to protozoan strains was developed and is described herein.     

A standardized format for handling data on plasmids,viruses and transposons: The PVT database format

The PVT format described here has been designed to store and retrieve genetic data on plasmids, viruses or transposons with special focus on their applications. Both naturally-occurring and engineered elements can be included in it. A variety of data can be accommodated in fields that are grouped in blocks: name and type of element, database administration, element administration, history, propagation, selection and host, biological properties, cloned insert and applications. The number of fields, now 157, can be expanded as required. Most properties can be described in simple logical fields. The format is organized to permit rapid searches and to facilitate communication between database and user; connection with culture and/or DNA collections is also envisaged and adequate fields for these tasks have been provided. The format allows cross-reference with that originated by the Microbial Information Network Europe (MINE) for computer storage and handling of bacterial or fungal strain data.     

Long-Term Preservation and Storage of Mycobacteria

Under contract with the National Institute of Allergy and Infectious Diseases, the Trudeau Mycobacterial Culture Collection has been greatly expanded to provide for the scientific community a collection of representative strains of mycobacteria of biomedical importance. Problems concerned with the preparation, bottling, and distribution of such organisms have been dealt with and are detailed in this paper. Examination of collected data revealed that the temperature of storage and not the suspending menstruum was more important for prolonged survival of mycobacteria stored at subzero temperatures. For optimum results, mycobacteria may be suspended either in Dubos Tween-albumin broth or in Middlebrook 7H-9 liquid medium supplemented with ADC enrichment (commercial sources used) and stored at -70 C. Either of these suspending fluids supplied a growth-supporting medium for cultures which must be shipped long distances, often without refrigeration. To avoid sublimation of suspending medium during prolonged storage at -70 C (a problem inherent in many screw-capped containers), we have chosen to use vaccine-stoppered serum bottles sealed with aluminum crimp caps. The methods described have provided suspensions with (i) excellent viability over prolonged periods of storage, (ii) stable metabolic activities, and (iii) highly reproducible inocula for animal experiments.     

The PEDANT genome database

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRS data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein-protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics.