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PubMedDate not supplied

A case study of the evolving software architecture for the FDA generic drug application process.

This primary goal of this project was to develop a software architecture to support the Food and Drug Administration (FDA) generic drug application process by making it more efficient and effective. The secondary goal was to produce a scalable, modular, and flexible architecture that could be generalized to other contexts in interorganizational health care communications. The system described here shows improvements over the old system for the generic drug application process for most of the defined design objectives. The modular, flexible design that produced this new system offers lessons for the general design of distributed health care information systems and points the way to robust application frameworks that will allow practical development and maintenance of a distributed infrastructure.

Drug Approval↗

PubMed2005

FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform.

BACKGROUND: Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. RESULTS: Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. CONCLUSION: The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.

Automation↗

PubMed2005

SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

BACKGROUND: Single nucleotide polymorphisms (SNPs) provide an important tool in pinpointing susceptibility genes for complex diseases and in unveiling human molecular evolution. Selection and retrieval of an optimal SNP set from publicly available databases have emerged as the foremost bottlenecks in designing large-scale linkage disequilibrium studies, particularly in case-control settings. RESULTS: We describe the architectural structure and implementations of a novel software program, SNPHunter, which allows for both ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data, including physical position, function class, flanking sequences at user-defined lengths, and heterozygosity from NCBI dbSNP. The SNP data extracted from dbSNP via SNPHunter can be exported and saved in plain text format for further down-stream analyses. As an illustration, we applied SNPHunter for selecting SNPs for 10 major candidate genes for type 2 diabetes, including CAPN10, FABP4, IL6, NOS3, PPARG, TNF, UCP2, CRP, ESR1, and AR. CONCLUSION: SNPHunter constitutes an efficient and user-friendly tool for SNP screening, selection, and acquisition. The executable and user's manual are available at http://www.hsph.harvard.edu/ppg/software.htm

Algorithms↗

PubMedDate not supplied

An approach for the evaluation of software engineering environments in medicine.

This article examines several criteria for the evaluation of software engineering environments (SEE) in medicine. The study is restricted to the evaluation of the SEE itself, not of its by-products which are the medical applications developed with the SEE. Basic principles for an evaluation methodology are presented. They consist in determining the evaluation objectives and judging a SEE according to criteria which are grouped into three broad categories--functional, generic and environmental. Each category reflects a particular domain of evaluation of the SEE. Methods of measurement and questions highlighting these specific areas are mentioned. Criteria are extracted from the list of objectives that follows the HELIOS European AIM project of the Commission of the European Communities. Special emphasis is drawn on the criteria for which the medical specificity and usefulness of a SEE can be approach. For this purpose a method of measurement of such appropriateness is proposed.

Attitude to Computers↗

PubMed2006

Using ethnographic methods to carry out human factors research in software engineering.

This article describes how ethnographic methods were used to observe and analyze student teams working on software engineering (SE) projects. The aim of this research was to uncover the effects of the interplay of different personality types, as measured by a test based on the Myers-Briggs Type Indicator (MBTI), on the workings of an SE team. Using ethnographic methods allowed the researchers to record the effects of personality type on behavior toward teammates and how this related to the amount of disruption and positive ideas brought forward from each member, also examined in detail were issues that were either dogged by disruption or that did not have sufficient discussion devoted to them and the impact that they had on the outcomes of the project. Initial findings indicate that ethnographic methods are a valuable weapon to have in one's arsenal when carrying out research into human factors of SE.

Anthropology, Cultural↗

PubMed2000

[Development of DICOM image viewing software for efficient image reading and evaluation of distributed server system for diagnostic environment].

To construct an efficient diagnostic environment using computer displays, the author investigated the time of network transmission using clinical images. In our hospital, we introduced optical-fiber 100Base-Fx Ethernet connections between 22 HIS-segments and one RIS-segment. Although Ethernet architecture is inexpensive, the speed of image transmission becomes 2371 KB/sec. (4.6 CT-slice/sec.) in the RIS-segment and 996 KB/sec. (1.9 CT-slice/sec.) from the RIS-segment to HIS-segments. Because one examination is transmitted in one minute, it does not disturb image reading. Otherwise, a distributed server system using inexpensive personal computers helps in constructing an efficient system. This investigation showed that commercially based Digital Imaging and Communications in Medicine(DICOM) servers and RSNA Central Test Node servers are not so different in transmission speed. The author programmed and developed DICOM transmission and viewing software for Macintosh computers. This viewer includes two inventions, dynamic tiling window system (DTWS) and window binding mode(WBM). On DTWS, windows, tiles, and images are independent objects, which are movable and resizable. The tile-matrix is changeable by mouse dragging, which realizes suitable tile rectangles for wide-low or narrow-high images. The arranging window tool prevents windows from scattering. Using WBM, any operation affects each window similarly. This means that the relationship of compared images is always equivalent. DTWS and WBM contribute greatly to a filmless diagnostic environment.

Computer Communication Networks↗

PubMed2003

[Software for MR image reconstruction from data acquired on an irregular k-space trajectory].

A PC-based software was developed and programmed with VC++6 for reconstructing MR images from the data acquired on an irregular k-space trajectory. It can read clinical MRI raw data and image data, create numerical phantoms, design k-space trajectories, generate k-space data from numerical phantom, calculate weighting functions, reconstruct images, and carry out error analysis for the reconstructed images. It is helpful to the investigations of new k-space trajectories and new reconstruction algorithms.

Algorithms↗

PubMed2005

OLINDA/EXM: the second-generation personal computer software for internal dose assessment in nuclear medicine.

UNLABELLED: The OLINDA/EXM version 1.0 personal computer code was created as a replacement for the widely used MIRDOSE3.1 code. This paper documents the basic function of the code and how it is similar to and different from the MIRDOSE software. METHODS: After creation of the code and alpha- and beta-testing phases, a premarket notification submission (510(k)) was filed with the Food and Drug Administration to permit marketing of the code. Permission was granted in June 2004, and the code is currently being distributed through Vanderbilt University. Not all of the technical details of the dosimetry methods have been shown here, as they have been previously documented. RESULTS: Agreement of doses between the MIRDOSE3.1 and OLINDA/EXM codes was good, within 1%-2% in most cases. CONCLUSION: The extensive testing of the OLINDA/EXM code, based on comparison with literature-established dose calculations and with the widely tested and accepted MIRDOSE3.1 code, should give users confidence in its output. The OLINDA/EXM code should be easy for MIRDOSE users to adopt and for new users to understand. It will be useful in standardizing and automating internal dose calculations, assessing doses in clinical trials with radiopharmaceuticals, making theoretic calculations for existing pharmaceuticals, teaching, and other purposes.

Nuclear Medicine↗

PubMed1991

Electrophoretic gel image analysis software for the molecular biology laboratory.

We present GelReader 1.0, a microcomputer program designed to make precision, digital analysis of one-dimensional electrophoretic gels accessible to the molecular biology laboratory of modest means. Images of electrophoretic gels are digitized via a desktop flatbed scanner from instant photographs, autoradiograms or chromogenically stained blotting media. GelReader is then invoked to locate lanes and bands and generate a report of molecular weights of unknowns, based on specified sets of standards. Frequently used standards can be stored in the program. Lanes and bands can be added or removed, based upon users' subjective preferences. A unique lane histogram feature facilitates precise manual addition of bands missed by the software. Image enhancement features include palette manipulation, histogram equalization, shadowing and magnification. The user interface strikes a balance between program autonomy and user intervention, in recognition of the variability in electrophoretic gel quality and users' analytical needs.

Computer Peripherals↗

PubMed1990

A two-dimensional acrylamide gel electrophoresis/computer software approach to decoding the human genome.

The human genome sequencing initiative is sure to be an expensive and time-consuming project. To maximize the quality of the initial thrust, it is necessary to concentrate on sequencing those genes that are actively involved in crucial biological processes, both normal and otherwise. To identify the protein products of these genes, we propose the use of two-dimensional acrylamide gel electrophoresis and powerful computer software. The two-dimensional gels can then be scaled to yield sufficient amounts of the protein for direct amino acid sequence analysis. The amino acid sequence then provides the direct link back to the gene.

Amino Acid Sequence↗

PubMed1988

[Innovations in computerized tomography: software routines and their relevance for mummy research and anthropology].

The application of computed tomography (CT) has been proved to be useful not only in present-day medicine, but also in non-clinical disciplines, as it is mummy research and physical anthropology. Concerning these fields CT-high-tech-innovations as three-dimensional surface reconstruction, dual energy/bone mineral-density--and metal artefact correction-programs are introduced and partly exemplified by investigation of human remains from ancient Egypt. The results point out that specific problems can be cleared up, which otherwise could be solved by means of destructive methods only. It is expected that future development of the mentioned CT-software helps to broaden its applicability.

Anthropology, Physical↗

PubMed1999

Comparison of COBE Spectra software version 4.7 PBSC and version 6.0 auto PBSC program.

Until recently, the collection of peripheral blood progenitor cells (PBPC) has been semi-automated by using the COBE Spectra, with the operator manually maintaining the position of the white cells being collected. The COBE Spectra Version 6.0 apheresis device offers the user an automated program for the collection of PBPC. In this study, we compared the new software Version 6.0 to that of Version 4.7. Patients (n = 46) undergoing PBPC collection were allocated to cell processing with either Version 4.7 (n = 24) or Version 6.0 (n = 22). The CD34+ cell count, mononuclear cell (MNC) count, white cell count (WCC), hemoglobin (Hb), and platelet content in the autograft product by using the two versions were compared. We divided the analysis into three subsets according to peripheral blood (PB) CD34 content: <10x10(6)/L, 10-50x10(6)/L and >50x10(6)/L. Analysis of the three subsets showed no statistical difference between results obtained when the starting PB CD34+ cell count was 10-50x10(6)/L (P=0.08) or >50x10(6)/L (P=0.4065). At lower starting PB CD34+ cell counts of <10x10(6)/L, Version 4.7 was superior (P=0.0167). However, autograft platelet contamination of the autograft was significantly higher using Version 4.7 (P=<0.0001).

Antigens, CD34↗

PubMed2000

Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry.

SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (MS/MS), which was initially developed for the automated interpretation of high-energy collision-induced dissociation (CID) MS/MS spectra of peptides, has been applied to the interpretation of low-energy CID and post-source decay (PSD) spectra of peptides. Based on peptide backbone fragmented ions and their related ions, which are the dominant ions observed in the latter two techniques, the types of ions and their propensities to be observed have been optimized for efficient interpretation of the spectra. In a typical example, the modified SeqMS allowed the complete sequencing of a 31-amino acid synthetic peptide, except for the isobaric amino acids (Leu or Ile, and Lys or Gln), based on only the low-energy CID-MS/MS spectrum.

Amino Acid Sequence↗

PubMed2000

Novel hotspot detector software reveals a non-CpG hotspot of germline mutation in the factor IX gene (F9) in Latin Americans.

Two-base substitutions at each of two nucleotides in the factor IX gene (F9), but not part of CpG dinucleotides, were recently reported in a small population sample collected in Mexico, a significant observation of recurrent sites ("hotspots") of mutation (P=0.00005). When these new data were combined with previously collected mutation data into two progressively larger and inclusive Latin American samples, additional mutations were observed at one recurrent site, nucleotide 17747, and an additional recurrent nucleotide was observed such that the recurrent nucleotides in these larger samples were also significant (P=0.0003 and 0.0003). In contrast, in three non-Latin American control samples, there was at most only one nucleotide that recurred only once, most likely a chance recurrence (P>/=0.5). When the significance of substitutions was analyzed at each recurrent nucleotide individually, nucleotide 17747 was shown to be a significant recurrent nucleotide by itself in all the Latin American population samples (P</=0.02). Furthermore, a standard statistical comparison of mutation frequencies in the previously collected data alone confirmed that the frequency of mutation at nucleotide 17747 is significantly higher in Latin Americans than in all other populations combined (P=0.01). Thus, nucleotide 17747 is a germline mutation hotspot in F9 specific to Latin American populations. This may be the first evidence for population-specific effects on germline mutation that causes human genetic disease. The significance of the observed recurrent sites was analyzed using new software called Hotspot Detector which is capable of detecting significant recurrent sites in small samples, extending the sensitivity of F9 as a human germline mutagen test. Hotspot Detector uses a Monte-Carlo simulation method that was validated by comparing its results with those from an exact probability formula derived from statistical theory.

CpG Islands↗

PubMed2001

GlycoMod--a software tool for determining glycosylation compositions from mass spectrometric data.

GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein-derived oligosaccharide comprised of either underivatised, methylated or acetylated monosaccharides, or with a derivatised reducing terminus. The composition of a glycan attached to a peptide can be computed if the sequence or mass of the peptide is known. In addition, if the protein is known and is contained in the SWISS-PROT or TrEMBL databases, the program will match the experimentally determined masses against all the predicted protease-produced peptides (including any post-translational modifications annotated in these databases) which have the potential to be glycosylated with either N- or O-linked oligosaccharides. Since many possible glycan compositions can be generated from the same mass, the program can apply compositional constraints to the output if the user supplies either known or suspected monosaccharide constituents. Furthermore, known oligosaccharide structural constraints on monosaccharide composition are also incorporated into the program to limit the output.

Carbohydrate Sequence↗

PubMed1986

Toward computerized morphometric facilities: a review of 58 software packages for computer-aided three-dimensional reconstruction, quantification, and picture generation from parallel serial sections.

This review gives an inventory of 58 computer-aided three-dimensional reconstruction applications in the domain of biomedical research. It is devoted to the formulation of a set of recommendations thought to be necessary for improved performance of software packages in this field. These recommendations can be used to select packages and to guide future developments of existing reconstruction systems. The survey is restricted to three-dimensional reconstructions based upon a series of parallel sections of an object. Subjects treated are programming languages, resolution and sampling, input preparation, realignment, local deformation of slices, numerical quantifications, topological complexity, internal representation, display complexity (hidden surfaces, shading, smoothing), structure extraction, descriptive elements, database, data compression, time efficiency of systems and algorithms, hardware configuration, input devices, input media, interactive aids, display devices, and output devices. Information for this survey comes from articles that appeared between 1965 and 1985.

Computers↗

PubMed2005

Software system for three-dimensional volumetric reconstruction of histological sections: a case study for the snake chondrocranium.

Volumetric digital computer-assisted reconstruction of histological sections is an attractive possibility for developmental studies. Commercial solutions are very expensive for many educational institutions. Therefore, we developed a software system for three-dimensional reconstruction of anatomical virtual models. The input data for the system are the digitized images from the histological samples of the chondrocranium of two crotalines, Bothrops jararaca and Crotalus durissus terrificus, and one colubrid, Philodryas olfersii, using a stereomicroscope connected to a digital camera. These images are then manually registered and segmented. We use computer graphics visualization algorithms such as marching cubes and ray casting to generate three-dimensional visualizations of the volumes. The results show that the digital reconstruction is as good as the manual reconstruction with the advantages of speed of reconstruction, accuracy, and flexibility to handle and study the volume. Compared with commercial options, our system has approximately the same features, and it is available free for the scientific community.

Animals↗

PubMed1993

An integrated software system for quality assurance-related kappa coefficient analysis of intraoperative transesophageal echocardiography interpretive skills.

This report describes the development of a quality assurance-oriented integrated software system designed for an anesthesiology-based intraoperative transesophageal echocardiography service. Entry data include patient and operation demographics, two-dimensional echocardiographic, saline-contrast, and color flow/pulsed Doppler assessments of the heart and great vessels, presented in a defined sequence. A statistical analysis component (kappa coefficient analysis) allows for comparison of intraoperative real-time interpretations with laboratory interpretations made by experienced full-time echocardiographers on a field-by-field basis. This provides a means of quantifying expertise in each individual aspect of the patient examination sequence. We believe that such self-appraisal data are essential for delineating the status and tracking the progress of service being provided.

Echocardiography, Transesophageal↗