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PubMed2006

SBMLToolbox: an SBML toolbox for MATLAB users.

SUMMARY: We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML. AVAILABILITY: SBMLToolbox is freely available from http://sbml.org/software/sbmltoolbox

Computer Simulation↗

PubMed1990

[Personal laboratory data management system using optical card].

This paper describes the development and state of the medical optical card system. Recently, computerized medical information systems have been developed in many hospitals and they allow quick access and automatic processing of the patient's data in medical practice and research. However, the use of the information stored by such a system has been limited to each hospital while it is not rare for a patient to change hospitals. It is desirable to develop a personal medical data management system which allows the patient to carry his own medical records for a long period of time, and hospitals to share the information about the patient. The optical card is a transportable information medium with a large capacity. Since data are recorded optically with a laser beam, the card is tolerant to environmental factors such as static electricity, magnetism and impact which injure other transportable media such as IC card, magnetic stripe card and floppy disk. Therefore, the optical card suits our purpose. We developed a prototype of the medical optical card system. In our system, the card can contain character data, numerical data, two-valued image data and electrocardiographical data. In order to share laboratory data among different database systems, we defined a data descriptive language which enables complete and compact data description without any external code tables. The recorded patient data are presented in the original multi-window system, which allows the doctor to see any combination of any part of the patient's information simultaneously.

Clinical Laboratory Information Systems↗

PubMedDate not supplied

Computerized data bank system for temporal bone histopathology.

A computerized data bank system to store and analyze temporal bone histopathologic data is described. This system uses the University of Pittsburgh's Digital Equipment Corporation System 10 computer and the System 1022 data base management software. Data on histology cases are divided into five files: general information, otologic information, summary, histopathologic information about the external ear and middle ear, and histopathologic information about the inner ear. Eleven general terms are used to describe pathologic findings, surgery, postmortem degeneration, and artifacts. In addition, provision is made for the inclusion of more precise qualitative information to be entered as text.

Computer Systems↗

PubMed1994

A novel search method for protein sequence--structure relations using property profiles.

In protein engineering and design it is very important that residues can be inspected in their specific environment. A standard relational database system cannot serve this purpose adequately because it cannot handle relations between individual residues. With SCAN3D we introduce a new database system for integrated sequence and structure analysis of proteins. It uses the relational paradigm wherever possible. Its main power, however, stems from the ability to retrieve stretches of consecutive residues with certain properties by comparing a property profile with all stretches of residues in the database, exploiting the ordered character of proteins. In doing so, it bypasses the large number of join operations that would be required by relational database systems. An additional advantage of using property profile matching is that searches can be carried out allowing a pre-set number of mismatches. Also, as the database is read-only, SCAN3D does not need interactive data update mechanisms. Queries typical of a molecular engineering environment are demonstrated with specific examples: analysis of peptides that induce local structure, analysis of site-dependent rotamers and residue--residue contact analysis.

Amino Acid Sequence↗

PubMed2005

Metabolites and pathway flexibility.

Flexibility of metabolites and enzymes is investigated (i) on the level of the individual molecule, (ii) on the pathway level and (iii) combined effects on the systems and network level. Tools and results from our current research are summarized including data from our metabolite enzyme database. Including our latest census we find frequently used metabolites stimulate evolutionary flexibility in specific enzyme superfamilies. Furthermore, simultaneous changes of reactions and metabolites are observed in these flexible enzyme superfamilies. Both effects provide a strong source for resistance in parasites and pathogens. Specific adaptations scenarios and some counter strategies are discussed.

Catalysis↗

PubMed2004

A local alignment metric for accelerating biosequence database search.

We introduce a metric for local sequence alignments that has utility for accelerating optimal alignment searches without loss of sensitivity. The metric's triangle inequality property permits identification of redundant database entries guaranteed to have optimal alignments to the query sequence that fall below a specified score threshold, thereby permitting comparisons to these entries to be skipped. We prove the existence of the metric for a variety of scoring systems, including the most commonly used ones, and show that a triangle inequality can be established as well for nucleotide-to-protein sequence comparisons. We discuss a database clustering and search strategy that takes advantage of the triangle inequality. The strategy permits moderate but significant acceleration of searches against the widely used "nr" protein database. It also provides a theoretically based method for database clustering in general and provides a standard against which to compare heuristic clustering strategies.

Algorithms↗

PubMed2005

[KIS-RIS-PACS integration: the Marburg approach].

When describing the development of data processing at the Department of Radiology at the Philipps University of Marburg, three phases can be identified covering the areas of patient care, education, and research as well as administrative and organizational aspects. The first phase (1987-1995) was centered on radiology and characterized by the early implementation of the radiology information system (RIS) and installation of a picture archiving and communication system (PACS). The experiences gained during this phase led to intensive discussion on application-oriented information processing. The second phase (1996-2000) describes the changes in the general framework brought by Internet technology and international standards. The course was set for the future of data processing in the hospital setting. The phase ended with implementation of a clinical workplace system (KAS) as the basis for a comprehensive electronic patient record and the switch in radiology to an integrated RIS solution. The third phase (2001-2006) addressed further implementation and development of clinical data management in which both regular documentation of patient data and information processing not related to patients are optimized by making use of Intranet/Internet technology. It includes the hospital wide implementation of PACS and the forthcoming phase of information processing increasingly shaped by workflow and decision support.

Database Management Systems↗

PubMed2004

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.

The immense growth in the volume of research literature and experimental data in the field of molecular biology calls for efficient automatic methods to capture and store information. In recent years, several groups have worked on specific problems in this area, such as automated selection of articles pertinent to molecular biology, or automated extraction of information using natural-language processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing on multiple sources of information to infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information.

Artificial Intelligence↗

PubMed2001

A comparison of microarray databases.

Microarray technology has become one of the most important functional genomics technologies. A proliferation of microarray databases has resulted. It can be difficult for researchers exploring this technology to know which bioinformatics systems best meet their requirements. In order to obtain a better understanding of the available systems, a survey and comparative analysis of microarray databases was undertaken. The survey included databases that are currently available, as well as databases that should become available in early 2001. Databases fall into three categories: (i) those that can be installed locally, (ii) those available for public data submission and (iii) those available for public query. Developers of microarray gene-expression databases were asked questions regarding the scope and availability of their database, its system requirements, its future compliance with MGED (Microarray Gene Expression Database) standards, and its associated analytical tools. Participants included AMAD (Stanford/Berkeley/UCSF), ArrayExpress (EBI), ChipDB (MIT/Whitehead), GeneX (NCGR), GeNet (Silicon Genetics), GeneDirector (BioDiscovery), GEO (NCBI), GXD (Jackson Laboratory), mAdb (NCI), maxdSQL (University of Manchester), NOMAD (UCSF), RAD (University of Pennsylvania) and SMD (Stanford University). Other database developers were contacted but data was not available at the time of manuscript preparation. Each database fulfils a different role, reflecting the widely varying needs of microarray users.

Animals↗

PubMed2003

Development of an integrated laboratory information management system for the maize mapping project.

MOTIVATION: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, researchers need an efficient way to interact with genetic mapping software and with data files from automated DNA sequencing. They also need ways to manage primer data for mapping and sequencing and provide views of the integrated physical and genetic map and views of genetic map comparisons. RESULTS: The MMP-LIMS system has been used successfully in a high-throughput mapping environment. The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers have been entered and verified via MMP-LIMS. The system is flexible, and can be easily modified to manage data for other species. The software is freely available. AVAILABILITY: To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.

Chromosome Mapping↗

PubMed2006

Argonaute--a database for gene regulation by mammalian microRNAs.

MicroRNAs (miRNAs) constitute a recently discovered class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational inhibition. They are involved in diverse processes, including cellular differentiation, proliferation and apoptosis. Recent evidence also suggests their importance for cancerogenesis. By far the most important model systems in cancer research are mammalian organisms. Thus, we decided to compile comprehensive information on mammalian miRNAs, their origin and regulated target genes in an exhaustive, curated database called Argonaute (http://www.ma.uni-heidelberg.de/apps/zmf/argonaute/interface). Argonaute collects latest information from both literature and other databases. In contrast to current databases on miRNAs like miRBase::Sequences, NONCODE or RNAdb, Argonaute hosts additional information on the origin of an miRNA, i.e. in which host gene it is encoded, its expression in different tissues and its known or proposed function, its potential target genes including Gene Ontology annotation, as well as miRNA families and proteins known to be involved in miRNA processing. Additionally, target genes are linked to an information retrieval system that provides comprehensive information from sequence databases and a simultaneous search of MEDLINE with all synonyms of a given gene. The web interface allows the user to get information for a single or multiple miRNAs, either selected or uploaded through a text file. Argonaute currently has information on 839 miRNAs from human, mouse and rat.

Animals↗

PubMed2004

A database designed to computationally aid an experimental approach to alternative splicing.

A unique microarray approach has been developed to profile alternative splicing in the cell. To support the development of this approach, we have developed the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is a unique alternative splicing information resource designed specifically with experimentalists in mind. MAASE is an online resource for the convenient access, identification, and annotation of alternative splicing events (ASEs). MAASE consists of two components: an annotation system and a curated database. The annotation system is a web-based workspace that combines manual and computational approaches to identifying and annotating ASEs, a combination that is vital if a comprehensive collection is to be obtained. The annotation system is publicly available and provides a scalable solution to acquiring as well as contributing to annotated ASEs. MAASE annotated ASEs are deposited into the database component, which can either be queried one entry at a time or multiple entries at a time with convenient access to alternatively spliced junctional and surrounding sequences to facilitate the design of microarray experiments.

Alternative Splicing↗

PubMedDate not supplied

A database manager of biomedical images.

In order to allow an efficient archiving and retrieval of biomedical images, PACS would include an image DBMS. As biomedical images have complex structures we developed a specific DBMS over a relational one. The medical image database manager ensures a data description that takes into account data semantics so that consistency or existential constraints may be verified. It provides a unique language to retrieve images no matter what their storage format. It encompasses the queries of the user which constitute a filter over associated data. The manager can handle changes in the environment of the image. We implemented a manager prototype to show the validity of logical access possibilities. The user need no longer know the structure of the image database to access data. The logical access allows retrieval of images, whatever the architecture of the base. An automatic query construction consists of three functional levels including the interfaces towards the external environment which ensure a logical independence from the database, a query generator which creates the correspondence between the user's query and physical access queries, a dictionary which contains the structure of the image data and consistency constraints.

Computer Systems↗

PubMed2002

The Mouse Genome Database (MGD): the model organism database for the laboratory mouse.

The Mouse Genome Database (MGD) is the community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology and disease (http://www.informatics.jax.org). MGD strives to provide a highly curated, highly integrated information resource that not only includes the consensus view of current knowledge about the mouse, but also provides comparative genomic information particularly for human and rat genomes. MGD includes extensive information about mouse genes, supporting all gene attribute assertions with experimental data, statements of evidence and citation. Detailed information about alleles and mouse mutants includes genotype, molecular variant and phenotype descriptions. Extensive collaboration with other data providers such as NCBI, RIKEN and SWISS-PROT provides standardization of gene:sequence associations and robust interconnections between large information systems based on shared sequence curation. Recent integration of large datasets of mouse full-length cDNAs and radiation-hybrid mapped ESTs, the continued development and use of extensive structured vocabularies and the expansion of the representation of phenotypes highlight this year's developments.

Alleles↗

PubMed2005

MINERVA: a multi-modality plugin-based radiation therapy treatment planning system.

Researchers at the INEEL, MSU, LLNL and UCD have undertaken development of MINERVA, a patient-centric, multi-modal, radiation treatment planning system, which can be used for planning and analysing several radiotherapy modalities, either singly or combined, using common treatment planning tools. It employs an integrated, lightweight plugin architecture to accommodate multi-modal treatment planning using standard interface components. The design also facilitates the future integration of improved planning technologies. The code is being developed with the Java programming language for interoperability. The MINERVA design includes the image processing, model definition and data analysis modules with a central module to coordinate communication and data transfer. Dose calculation is performed by source and transport plugin modules, which communicate either directly through the database or through MINERVA's openly published, extensible markup language (XML)-based application programmer's interface (API). All internal data are managed by a database management system and can be exported to other applications or new installations through the API data formats. A full computation path has been established for molecular-targeted radiotherapy treatment planning, with additional treatment modalities presently under development.

Body Burden↗

PubMed1993

A method for selecting data subsets from large medical data bases.

Because of the exponential increase in health care expenditures, attention has been drawn to the cost and effectiveness of health care delivered. The use of electronic data bases as a means for assessing health care effectiveness has been advocated as powerful computer systems have become commonplace. The need to work efficiently with extremely large data bases presents difficult challenges to researchers who wish to focus on specific aspects of the data. This paper describes a computer program written to facilitate the analysis of large medical data sets by providing a straightforward way to specify and select data subsets from the aggregate data base.

Centers for Medicare and Medicaid Services, U.S.↗

PubMed2003

SNPCEQer II: the integrated detection and analysis of SNPs in DNA sequences.

SNPCEQer II is a graphical user interface (GUI)-based application that integrates single nucleotide polymorphism (SNP) detection, SNP analysis and SNP editing in the Microsoft Windows (R) environment. SNPCEQer II detects SNPs in DNA sequences generated by the Beckman CEQ TM 2000 XL DNA analysis system. It provides tools to analyse SNPs by inspecting and comparing trace data (chromatograms) around putative SNPs with that of other related DNA sequences, and it can search for those SNPs in the National Center for Biotechnology Information (NCBI) databases. SNPCEQer II can determine the mutation type of a coding SNP and generate data for submission to the dbSNP database. The SNP report can be edited and printed, as can the chromatograms. SNPCEQer II is implemented in Visual C++.

Algorithms↗

PubMed1997

Three perspectives on work-related injury surveillance systems.

This paper reviews surveillance approaches for occupational injuries and evaluates three emerging methodologies for the enhancement of work-related injury surveillance: (1) narrative data analysis, (2) data set linkage, and (3) comprehensive company-wide surveillance systems. All three methods are the result of new applications of computer hardware and software that have apparent strengths and limitations. A major strength is the improved description of work exposures and related injuries leading to better understanding of injury etiology. This understanding, however, is limited by the data quality and completeness entered on records at the time of the injury. We recommend (1) more widespread inclusion of narrative text in databases, analyses of which can be a valuable supplement to injury coded data; (2) the increased use of data set linkage studies to combine injury and work-history data; and (3) the development of comprehensive company-wide surveillance systems to expedite the use of epidemiologic data for occupational injury prevention activities. Further development of these methods and others is encouraged, especially in light of technological advancements in data capture, analysis and presentation. Only through such efforts can we best apply epidemiologic principles to preventing injuries in the workplace.

Accidents, Occupational↗