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PubMed1993

Automated production of high density cosmid and YAC colony filters using a robotic workstation.

We report here on a system for automated preparation of high-density colony filters of arrayed libraries using the high density replicating system (HDR) for the Beckman Biomek 1000 robotic workstation. This system, consisting of a 96-pin tool, a sterilization station and controlling software, transfers samples from microplates onto target membranes in arrays up to 36 times the density of a 96-well microplate. The transfer operation can be completely automated with the addition of the Biomek Side Loader System, which consists of a robotic arm capable of transferring plates and filters between the Biomek working tablet and a storage area. Using the complete system, we are able to plate 32 replica filters (8 x 12 cm), each containing the clones from 16 different microplates (i.e., 1536 clones per filter), in a 16-h overnight run without any operator intervention. We describe conditions used for transfer of bacterial yeast colonies and fixation of DNA to the membranes, and we illustrate hybridization results obtained with cosmid and YAC filters.

Biotechnology↗
PubMed1995

A non-linear mathematical model for the in vivo evaluation of the RES phagocytic function.

A new non-linear mathematical model was constructed in order to perform in vivo quantification of the RES phagocytic function. This method is based on the same technical facilities as used for the routine liver-spleen scintigraphy with radiocolloids [1, 2]. But kinetic modeling of dynamic Tc-99m-sulfur colloid data produced estimations of the functional RE-parameters: the clearance rate of the colloidal particles, the rate of phagocytosis, and the RES functional volume, which can not be obtained by classical approaches. This non-linear model was designed on the basis of the principal characteristics of particulate material interaction with macrophages (attachment, phagocytosis, digestion) [3, 4, 5]. The theoretically examined behavior of this in vivo mathematical model corresponds with the experimental behavior of the RES. The mathematical expression of the dynamics is the system of non-linear differential equations with constant coefficients that have no analytical solution. Fitting of the normalized heart blood time-activity curve was obtained to identify the unknown model parameters via non-linear regression. For this purpose general interactive PASCAL procedure IDPAR for a PDP-11/34 computer was used (an IBM PC version is also available). Two to three iterations were needed to estimate the set of unknown parameters for any patient study (1-1.5 min). A very good fitting was obtained between experimental and model curves in every case of different pathologies (error of the approximation is about 2-3%). Studies were performed using an in vivo bolus injection of 3.6 mg/80 kg commercially available colloid KOREN labeled with 3m-Ci 99m-Tc (analog of TCK-1). Our method was used to determine the RES functional parameters for patient groups with different levels of the RES dysfunction. Obtained results illustrate the possibilities of our technique to quantitatively estimate not only great pathology (portal cirrhosis), but also small changes of the RE-function (case of hyperlipidemia and ulcer gaster). In all patient groups marked changes of Tc-99m-sulfur colloid turnover were observed. In general, tracer clearance from the circulation was decreased, and the rate of phagocytosis and the RES volume were diminished compared with controls. The effect of a reduction of phagocytosis increases when the RES dysfunction becomes stronger. It can be shown that a non-parametric Wilcoxon-Mann-Whitney test gives a significant difference (P95%) for these patient groups. Further, we represent the possibility of using the model for monitoring changes of the RES-function parameters during and after therapy. The quantitative test of the RES function can significantly enhance the diagnosis and management of different diseases. Serial colloidal studies may document changes in the RES-function for the tumors, cirrhosis, hyperlipidemia, reticulosis, hepatitis, thrombosis, infection, AIDS, burn injury, shock and trauma patients. The technique may be useful for the different RES investigations with laboratory animals. Created computer software can be used as a tool for kinetic models, simulation, and unknown parameters identification.

Humans↗
PubMed1995

Help: first aid issues.

First aid is the initial and immediate care given to a victim outside the hospital environment, with the purpose of assuring life and avoiding worsening conditions until he/she receives qualified assistance. Providing immediate aid to someone requires tranquility and, above all, knowledge on what has to be done or not in each situation. In addition to being treated by health professionals, the chances that a victim will receive early treatment by others are large. However, in Brazil, access to information, and the possibility of reviewing it whenever necessary, may contribute greatly to the process of assimilation of this knowledge, in addition to exercises on simulated cases. Informatics has been shown as an extremely useful tool in the development of educational software, considering its multiplicity of resources and providing for the users: motivation for an interactive experience, an individualized teaching that takes into account his/her own rhythm and desired complexity level, besides making possible the user's capacity for solving problems through simulated situations. Considering that, the number of individuals of the population prepared to act as First Aid helpers in situations of life threatening accidents or sudden illness is still very scarce. The ever increasing use of the computer as a mean of spreading information in schools, enterprises, and even households and considering the advantages of an educational software for the users regarding storage and retrieval of information when needed, we proposed the creation of an interactive teaching software. This software is being developed using Storyboard live. The methodology is the following: literature review, selection of images, development of the program, application tests. The initial selected issues are: assessment of the victim, cardiorespiratory arrest and resuscitation, airway obstruction, wounds, and hemorrhages. After utilizing the program, the user should be able to solve hypothetical situations with minimal initial care and maximal physical comfort for an accident or sudden illness victim.

Computer-Assisted Instruction↗
PubMed2004

Using Petri Net tools to study properties and dynamics of biological systems.

Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats.

Algorithms↗
PubMed2004

GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.

High-throughput gene expression analysis has become a frequent and powerful research tool in biology. At present, however, few software applications have been developed for biologists to query large microarray gene expression databases using a Web-browser interface. We present GENEVESTIGATOR, a database and Web-browser data mining interface for Affymetrix GeneChip data. Users can query the database to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs. Reversely, mining tools allow users to identify genes specifically expressed during selected stresses, growth stages, or in particular organs. Using GENEVESTIGATOR, the gene expression profiles of more than 22,000 Arabidopsis genes can be obtained, including those of 10,600 currently uncharacterized genes. The objective of this software application is to direct gene functional discovery and design of new experiments by providing plant biologists with contextual information on the expression of genes. The database and analysis toolbox is available as a community resource at https://www.genevestigator.ethz.ch.

Arabidopsis↗
PubMed1990

Computation of digitally reconstructed radiographs for use in radiotherapy treatment design.

The increasing use of 3-dimensional radiotherapy treatment design has created greater reliance on methods for computing images from CT data which correspond to the conventional simulation film. These images, known as computed or digitally reconstructed radiographs, serve as reference images for verification of computer-designed treatments. Used with software that registers graphic overlays of target and anatomic structures, digitally reconstructed radiographs are also valuable tools for designing portal shape. We have developed radiograph reconstruction software that takes full advantage of the contrast and spatial detail inherent in the original CT data. This goal has been achieved by using a ray casting algorithm which explicitly takes into account every intersected voxel, and a heuristic approach for approximating the images that would result from purely photoelectric or Compton interactions. The software also offers utilities to superimpose outlines of anatomic structures, field edges, beam crosshairs, and linear scales on digitally reconstructed radiographs. The pixel size of the computed image can be controlled, and several methods of interslice interpolation are offered. The software is written in modular format in the C language, and can stand alone or interface with other treatment planning software.

Humans↗
PubMed2003

BioWareDB: the biomedical software and database search engine.

UNLABELLED: A wealth of bioinformatics tools and databases has been created over the last decade and most are freely available to the general public. However, these valuable resources live a shadow existence compared to experimental results and methods that are widely published in journals and relatively easily found through publication databases such as PubMed. For the general scientist as well as bioinformaticists, these tools can deliver great value to the design and analysis of biological and medical experiments, but there is no inventory presenting an up-to-date and easily searchable index of all these resources. To remedy this, the BioWareDB search engine has been created. BioWareDB is an extensive and current catalog of software and databases of relevance to researchers in the fields of biology and medicine, and presently consists of 2800 validated entries. AVAILABILITY: BioWareDB is freely available over the Internet at http://www.biowaredb.org/

Abstracting and Indexing↗
PubMed2005

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

SUMMARY: Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually. AVAILABILITY: PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.

Algorithms↗
PubMed1997

SEALS: a system for easy analysis of lots of sequences.

We present a system of programs designed to facilitate sequence analysis projects involving large amounts of data. SEALS (System for Easy Analysis of Lots of Sequences) is a logically organized set of flexible, easily modifiable research tools, designed to run on open systems. Functionality is divided into approximately 50 commands which follow consistent syntax and semantics; wrappers are also provided for commonly used sequence analysis software to effect similar syntax for these programs. SEALS includes software for retrieving sequence information, scripting database search tools such as BLAST and MoST, viewing and analyzing search outputs, searching in and processing nucleotide and protein sequences using regular expressions, and constructing rational predictions of protein features. The system is designed to provide modular elements which can be combined, modified, and integrated with other methods in order to quickly design and execute computer experiments for sequence analysis projects at the scale of whole genomes.

Artificial Intelligence↗
PubMedDate not supplied

The PRIST-2 development environment: architecture and implementation.

The PRIST-2 system has been designed as an interactive and high-productivity tool for the rapid prototyping and development of medical applications. Three major issues were addressed in this research project which derived from the evolution of a previous 4th generation software package, called PRIST (patient record information system tool): a high transportability on different hardware and operating systems, a conversational and interactive user-interface and user-independence Relational Data Base Management System (RDBMS). Although we developed PRIST-2 on the top of the ORACLE RDBMS, it does not depend on SQL commercial products because the ORACLE features have been directly used only for SQL relational data base management. The application design methodology implemented in the system architecture allows an interactive and formal description of the application constraints in terms of the semantic data model rather than in terms of the data structure. The translation of the conceptual constraints into SQL tables is performed by several pre-defined routines. In the PC based release (MS/DOS, OS/2, Xenix operating systems), the Graphic-User Interface (GUI) has been developed using Microsoft Windows Software Development Kit. The UNIX release will use a GUI developed on top of the X-Windows environment.

Computer Graphics↗
PubMed2001

Integrating digital teaching-file systems with off-the-shelf presentation software to facilitate speaker-led conferences.

OBJECTIVE: Develop methods for automated transfer of images and associated text from a teaching-file repository into presentation material for speaker-led conferences. MATERIALS/METHODS: Our institution uses a Microsoft Windows (Microsoft Corp, Redmond, WA) software application to maintain a digital teaching-file database that can store and retrieve content in a case-centric fashion. Virtually any number of images can be stored with any given case. Cases and their associated images can be retrieved via a module that supports searches by American College of Radiology (ACR) code and by free-text Boolean queries on the history, findings, diagnosis, and discussion components of a case. In addition to the software system serving directly as an interactive teaching tool, the digital teaching file itself serves as an image repository and resource for attending radiologists who create their own presentations and lectures. To better support this use, software modules were developed for interprocess communication and automated creation of Powerpoint slides. These modules are fully integrated with the teaching-file software application. A single image or a set of selected images can be automatically made into individual slides with two mouse clicks. Images are automatically centered and optimally sized. A slide title is automatically rendered from the user's preference of the case history or diagnosis (stored with the case), or via the entry of freeform text. We describe the programming techniques that are used, as well as how several features of the operating system and Powerpoint itself can be integrated with a customized software application to facilitate this objective. RESULTS: The creation of presentation-ready Powerpoint slides is fully automated from within our teaching-file application, and the time required to create a presentation compared to the conventional method of manually seeking and inserting files from within Powerpoint itself, on a per-slide basis, is drastically reduced. The benefits are magnified by having all imagery stored within an organized and searchable database system so that desired images can be easily located. CONCLUSION: A digital teaching-file system can serve as a useful image repository for purposes ancillary to direct computerized instruction. Software that supports these uses, such as the automated creation of presentation material for speaker-led conferences, facilitates the radiologist's role as an educator.

Computer-Assisted Instruction↗
PubMed2004

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

BACKGROUND: Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. RESULTS: We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. CONCLUSIONS: Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

Algorithms↗
PubMed1991

Large database management in clinical dental research.

Previously the management and analysis of large databases for longitudinal clinical dental research has been severely restricted by the costs of custom-made software and access to suitable computing equipment. However, the recent availability of powerful personal computers and the use of the Scientific Information Retrieval Database Management System (SIR/DBMS) in association with BMDP Statistical Software has now created an enormously powerful tool for extensive and fast data manipulation requiring relatively few commands and the capability to easily perform detailed statistical analyses.

Computer Graphics↗
PubMed1993

Software for counting cells and estimating structural volumes with the optical disector and fractionator.

We describe MS-DOS software for the optical volume fractionator (OVF), a stereological method combining the principles of the optical disector (Gundersen et al.: Acta Pathol. Microbiol. Immunol. Scand., 96:857-881, 1988) and fractionator (Gundersen: J. Microsc., 143:3-45, 1986). The OVF program estimates the volume of a fixed and embedded structure, the numerical density of cells, and the total number of cells in a structure. The hardware requirements include a PC computer (386 or 486 with VGA graphics) and a conventional light microscope fitted with a rotating stage, extension tube, and length gauge. The software includes an introduction, tutorial, simulator, laboratory tool kit, and report generator. The tool kit improves the efficiency of gathering stereological data with light microscopy and offers a convenient link between the data of light and electron microscopy. A novel algorithm, based on fractionator sampling, gives the volume of a fixed and embedded structure from the same set of sections used for cell counting. A laboratory example illustrates the operation of the software.

Algorithms↗
PubMed2003

The NITE XML Toolkit: flexible annotation for multimodal language data.

Multimodal corpora that show humans interacting via language are now relatively easy to collect. Current tools allow one either to apply sets of time-stamped codes to the data and consider their timing and sequencing or to describe some specific linguistic structure that is present in the data, built over the top of some form of transcription. To further our understanding of human communication, the research community needs code sets with both timings and structure, designed flexibly to address the research questions at hand. The NITE XML Toolkit offers library support that software developers can call upon when writing tools for such code sets and, thus, enables richer analyses than have previously been possible. It includes data handling, a query language containing both structural and temporal constructs, components that can be used to build graphical interfaces, sample programs that demonstrate how to use the libraries, a tool for running queries, and an experimental engine that builds interfaces on the basis of declarative specifications.

Communication↗
PubMed2000

The PAUSE software for analysis of translational control over protein targeting: application to E. nidulans membrane proteins.

The PAUSE software has been developed as a new tool to study translational control over protein targeting. This makes it possible to correlate the position of clusters of rare codons in a gene, predicted to cause a translational pause, with the position of hydrophobic stretches in the encoded protein, predicted to span a membrane or to act as a cleavable signal for targeting to the secretory pathway. Furthermore, this software gathers these correlations over whole sets of genes. The PAUSE software is described here, and its use is illustrated on a set of membrane proteins from the fungus Emericella nidulans. Preferential distances of about 45 codons and of about 70 codons between putative transmembrane domains and predicted translational pauses were observed. Given that approximately 30 residues are required to span the large ribosomal subunit, the predicted pauses would therefore occur when the hydrophobic domain starts protruding from the ribosome ('+45 pause'), or fully protrudes as a hairpin ('+70 pause'). Thus, these specific pauses might reflect a translational control over membrane protein targeting or early recognition ('+45 pause'), and over insertion or folding ('+70 pause').

Aspergillus nidulans↗
PubMed2002

In silico determination of potential antisense targets for human beta-globin variants.

The functional characterization of available genomic sequences is the major task of the research in the post-genome era. This complex task requires an integrative approach of high-throughput systems with in vitro and in vivo models in order to have a reliable evaluation of the biological function. The oligonucleotide antisense technology is one of the most promising approaches for the investigation of gene function; the crucial point of antisense experiments is the identification of optimal target sites for hybridisation. In this paper we have applied a bioinformatic tool for the recognition of optimal antisense targets. In order to evaluate the effect of mutational events on target selection we have tested the program on a sample of human beta-hemoglobin variants. The proposed algorithm software will be integrated in a web based tool at the site: http://www.nettab.org/agewa.

Algorithms↗
PubMed1996

Educational challenges.

Despite the efforts of some educators, computers and electronic networks have yet to achieve their proper role in education. Advances, such as more intuitive software, CD-ROM media, and networks, offer powerful new tools, but technology is only one facet of instructional design. Much like effective authors of print media, software designers must adhere to certain principles that seem to underpin all successful computer-assisted instruction.

Computer Communication Networks↗