A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

Utility and features of a customized PC Windows-based relational database for managing microbial strain data

In addition to storing microbes, culture collections in industry, government or universities manage a vast and continuously expanding library of information on strain history and properties. An efficient and cost-effective computer database system is required for entering, analyzing and searching these data. This report describes the utility and features of a comprehensive database which consists of a commercially available relational database system combined with customized screens for data entry, viewing and report generation. The application was developed using Microsoft Access and Visual Basic to operate in the Windows environment on a local area network. Received 18 June 1997/ Accepted in revised form 21 November 1997     

BIOLUMBASE--the database of natural and transgenic bioluminescent organisms.

The Institute of Biophysics SB RAS hosts and maintains a specialized collection of luminous bacteria (CCIBSO 836) containing over 700 strains isolated in various regions of the world's oceans. The culture collection is a source of lux genes and biologically active substances. The wide application of bioluminescence in medicine and ecology has given importance to analysing information on the structure and functioning of bioluminescence systems in natural and transgenic microorganisms, as well as on their features that are closely interrelated with bioluminescence. The aims of our BIOLUMBASE database are: gathering information on microorganisms with lux genes, their analysis and free access, and distribution of this data throughout the global network. The database includes two sections, natural and transgenic luminous microorganisms, and is updated by our own experimental results, the published literature and internet resources. For the future, a publicly available internet site for BIOLUMBASE is planned. This will list the strains and provide comprehensive information on the properties and functions of luminous bacteria, the mechanisms of regulation of bioluminescence systems, constructs with lux genes, and applications of bioluminescence in microbiology, ecology, medicine and biotechnology. It is noteworthy that this database will also be useful for evaluation of biological hazards of transgenic strains. Users will be able to carry out bibliographic and strain searches starting from any feature of interest.     

白酒可培养微生物数据库构建

【目的】白酒可培养微生物的分离筛选是白酒行业重要的研究内容,本文旨在构建中国白酒生产环境中可培养微生物信息数据库。【方法】数据库信息主要来源于通过人工查阅和整理目前已发表的白酒微生物的相关的文献报道和菌种保藏中心相关的筛选自白酒生态系统的微生物信息。数据库主要设计3个功能:(1)白酒可培养微生物信息检索:通过菌株名称、分离位置、培养基、代谢产物等为条件检索相关的白酒可培养微生物信息,从而获取该白酒微生物详细的生理生化与分类学信息;(2)培养基信息检索:通过特定培养基成分,培养基编号和名称检索相关的培养基信息,包括培养的组成和配制方法。(3)数据更新:在线上传新的可培养微生物和培养基信息。【结果】目前数据库共收1221种白酒可培养微生物和295种培养基信息,网址为:http://cmbaijiu.i-sanger.com/。【结论】本数据库是我国白酒领域首个可培养微生物信息的数据库,将有助于白酒微生物培养的相关研究工作开展。     

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.     

Database of natural luminescent bacteria

The database of luminescent bacteria stored in the IBSO collection is one of the metasections of BIOLUMBASE. A logical schema of the metasection “Natural luminescent organisms”, classification of entities, and methods of attribute presentation have been developed. The database of luminescent bacteria maintained in the IBSO collection is being widened by findings of the collection staff as well as by information from scientific literature. The expectant contents of the database will be useful for resolving various problems of microbial ecology and biotechnology which deal with luminescent bacteria, luminescent system derived from them, and lux-genes cloned to other organisms. A potential user would be able not only to access cataloged data on strains but also to get information on properties, functions, use, and bibliography and to perform an attribute-match search of a strain.     

Using GIS to establish a public library consumer health collection

BACKGROUND: Learning the exact demographic characteristics of a neighborhood in which a public library serves, assists the collection development librarian in building an appropriate collection. Gathering that demographic information can be a lengthy process, and then formatting the information for the neighborhood in question becomes arduous.As society ages and the methods for health care evolve, people may take charge of their own health. With this prospectus, public libraries should consider creating a consumer health collection to assist the public in their health care needs. Using neighborhood demographic information can inform the collection development librarians as to the dominant age groups, sex, and races within the neighborhood. With this information, appropriate consumer health materials may be assembled in the public library. METHODS: In order to visualize the demographics of a neighborhood, the computer program ArcView GIS (geographic information systems) was used to create maps for specified areas. The neighborhood data was taken from the U.S. Census Department's annual census and library addresses were accumulated through a free database. After downloading the census block information from http://www.census.gov/geo/www/tiger/ the data was manipulated with ArcView GIS and queried to produce maps displaying the requested neighborhood demographics to view in respect to libraries. RESULTS: ArcView GIS produced maps displaying public libraries and requested demographics. After viewing the maps the collection development librarian can see exactly what populations are served by the library and adjust the library's collection accordingly. CONCLUSIONS: ArcView GIS can be used to produce maps displaying the communities that libraries serve, spot boundaries, be it "man-made or natural," that exist prohibiting customer service, and assist collection development librarians in justifying their purchases for a dedicated consumer health collection or resources in general.     

基于Oracle数据库的水稻病虫综合防治专家系统

应用数据库、计算机网络和空间信息技术,研制出基于Oracle数据库的“水稻病虫综合防治专家系统RIPMES Ⅱ”。系统包括数据采集、数据维护专家决策和GIS应用等子系统,能解决实时数据采集、海量数据存贮与分析、病虫害防治辅助决策、虫害空间分布特征分析等问题,是水稻病虫害综合防治的一个有效工具,同时也可为类似的专家系统的研究提供参考。     

Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the EcoCyc Database

The sets of compounds that can support growth of an organism are defined by the presence of transporters and metabolic pathways that convert nutrient sources into cellular components and energy for growth. A collection of known nutrient sources can therefore serve both as an impetus for investigating new metabolic pathways and transporters and as a reference for computational modeling of known metabolic pathways. To establish such a collection for Escherichia coli K-12, we have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database. The assembled collection revealed a substantial number of discrepancies between the high-throughput data sets, which we investigated where possible using low-throughput growth assays on soft agar and in liquid culture. We also integrated six data sets describing 16,119 observations of the growth of single-gene knockout mutants of E. coli K-12 into EcoCyc, which are relevant to antimicrobial drug design, provide clues regarding the roles of genes of unknown function, and are useful for validating metabolic models. To make this information easily accessible to EcoCyc users, we developed software for capturing, querying, and visualizing cellular growth assays and gene essentiality data.     

Efficient genetic markers for population biology

Population genetics has come of age. Three important components have come together: efficient techniques to examine informative segments of DNA, statistics to analyse DNA data and the availability of easy-to-use computer packages. Single-locus genetic markers and those that produce gene genealogies yield information that is truly comparable among studies. These markers answer biological questions most efficiently and also contribute to much broader investigations of evolutionary, population and conservation biology. For these reasons, single-locus and genealogical markers should be the focus of the intensive genetic data collection that has begun owing to the power of genetics in population biology.     

GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers

Extracting the desired data from a database entry for later analysis is a constant need in the biological sequence analysis community; GeneRecords 1.0 is a solution for GenBank biological flat file parsing, as it implements a structured representation of each feature and feature qualifier in GenBank following import in a common database managing system usable in a personal computer (Macintosh and Windows environments). This collection of related databases enables the local management of GenBank records, allowing indexing, retrieval and analysis of both information and sequences on a personal computer. AVAILABILITY: The current release, including the FileMaker Pro runtime application (built for Windows and Macintosh environments), is freely available at http://apollo11.isto.unibo.it/software/     

Development and application of computer software for cell culture laboratory management

Prototype computer software for a Cell Culture Laboratory Management System (CCLMS) has been developed to relieve cell culture specialists of the burden of manual recordkeeping. Conventional data archives in cell culture laboratories are prone to error and expensive to maintain. The reliance upon cell culture to provide models for biochemical and molecular biological research serves to magnify errors at great expense. The CCLMS prototype encapsulates a modular software application that manages the many aspects of cell culture laboratory recordkeeping. A transaction-based database stores detailed information on subcultures, freezes and thaws, prints waterproof labels for culture vessels, and provides for immediate historical trace-back of any cultured cell line. Linked database files store information specific to an individual culture flask while removing redundancy between similar groups of flasks. A frozen cell log maintains locations of all vials within any type of cryogenic storage unit, locates spaces for newly frozen cell lines, and generates alphabetical or numerical reports. Finally, modules for maintaining cell counts, user records, and culture vessel specifications to support a comprehensive automation process are incorporated within this software. The developed CCLMS prototype has been demonstrated to be an adaptable, reliable tool for improving training, efficiency, and historical rigor for two independent cell culture facilities.     

FunGene-DB: A web-based tool for Polyporales strains authentication

Polyporales are extensively studied wood-decaying fungi with applications in white and green biotechnologies and in medicinal chemistry. We developed an open-access, user-friendly, bioinformatics tool named FunGene-DB (http://www.fungene-db.org). The goal was to facilitate the molecular authentication of Polyporales strains and fruit-bodies, otherwise subjected to morphological studies. This tool includes a curated database that contains ITS1-5.8S-ITS2 rDNA genes screened through a semi-automated pipeline from the International Nucleotide Sequence Database (INSD), and the similarity search BLASTn program. Today, the web-accessible database compiles 2379 accepted sequences, among which 386 were selected as reference sequences (most often fully identified ITS sequences for which a voucher, strain or specimen, has been deposited in a public-access collection). The restriction of the database to one reference sequence per species (or per clade for species complex) allowed most often unequivocal analysis. We conclude that FunGene-DB is a promising tool for molecular authentication of Polyporales. It should be especially useful for scientists who are not expert mycologists but who need to check the identity of strains (e.g. for culture collections, for applied microbiology).     

AHMII: Agent to Help Microbial Information Integration

Reproducibility is the key to science. Therefore, the fidelity of organisms, particularly type strains, used in molecular biology must be authenticated before embarking on a series of experiments. In the case of microbes the authentic strain can be obtained from a culture collection. However, tracking down a culture collection that possesses the strain can be an arduous task. With this in mind we have developed a one-stop search engine for bacteria, fungi, yeasts and cell lines that indicates which collections carry the strain of interest. The search agent is named Agent to Help Microbial Information Integration (AHMII) and the URL address is http://www.wdcm.org/AHMII/ahmii.html.     

An off-line system for in-time analysis of cardiac catheterization data and for establishment of a cardiological database for retrospective studies.

The system described may be divided in two major parts: (i) automatic analysis of cardiac catheterization data running off-line on a Siemens 305 computer; (ii) storage and retrieval of the results from these analyses and additional data from related departments (thoracic surgery, internal medicine and clinical physiology) in a cardiological database on an IBM 370/155 computer. The first part is described with special regard to (i) operation and control during the phases of data collection, pre-processing, processing and storage of results; (ii) the presentation of the results in a complete and readable form and (iii) the modular design of the software. The results of an evaluation of the computer methods versus manual methods are also presented. The second part has been described with regard to the type of data entered in the cardiological database. The structure of the database and the programs used for storage and retrieval have not been described in detail in the present publication.     

HOWDY: an integrated database system for human genome research

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search.     

Data mining for simple sequence repeats in expressed sequence tags from barley,maize, rice,sorghum and wheat

Plant genomics projects involving model species and many agriculturally important crops are resulting in a rapidly increasing database of genomic and expressed DNA sequences. The publicly available collection of expressed sequence tags (ESTs) from several grass species can be used in the analysis of both structural and functional relationships in these genomes. We analyzed over 260000 EST sequences from five different cereals for their potential use in developing simple sequence repeat (SSR) markers. The frequency of SSR-containing ESTs (SSR-ESTs) in this collection varied from 1.5% for maize to 4.7% for rice. In addition, we identified several ESTs that are related to the SSR-ESTs by BLAST analysis. The SSR-ESTs and the related sequences were clustered within each species in order to reduce the redundancy and to produce a longer consensus sequence. The consensus and singleton sequences from each species were pooled and clustered to identify cross-species matches. Overall a reduction in the redundancy by 85% was observed when the resulting consensus and singleton sequences (3569) were compared to the total number of SSR-EST and related sequences analyzed (24606). This information can be useful for the development of SSR markers that can amplify across the grass genera for comparative mapping and genetics. Functional analysis may reveal their role in plant metabolism and gene evolution.