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PubMed2004

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

Computational Biology↗

PubMed2005

Preparation of cherry-picked combinatorial libraries by string synthesis.

String synthesis [1-3] is an efficient and cheap manual method for preparation of combinatorial libraries by using macroscopic solid support units. Sorting the units between two synthetic steps is an important operation of the procedure. The software developed to guide sorting can be used only when complete combinatorial libraries are prepared. Since very often only selected components of the full libraries are needed, new software was constructed that guides sorting in preparation of non-complete combinatorial libraries. Application of the software is described in details.

Combinatorial Chemistry Techniques↗

PubMed1994

Computerized tracking of mammography patients: value of a radiology information system integrated with a personal-computer data base.

OBJECTIVE. We investigated the advantages of using a radiology information system as the primary data source for a mammographic patient-tracking system that is based on a personal-computer local-area network and that requires almost no data entry. HARDWARE AND SOFTWARE. Our mammographic data base is maintained on a file server that provides cross-platform access to both Macintosh and IBM-compatible personal computers. Locally developed software automatically transfers mammographic data from our radiology information system to the file server's mammographic data base. The data transferred include patients' demographics (e.g., hospital identification number, address, referring physician) and the complete mammographic report. With the use of specific terminology, the need for follow-up can be automatically gleaned from the mammographic report and coded within the data base. Graphically oriented, commercially available software provides easy access to this information from any personal computer on our department's network. The software provides considerable flexibility for searching and manipulating the data without the need for customized data-base programming. Redundant data entry and associated errors are drastically reduced, as are personnel requirements for maintaining the system. Relative to most commercial radiology information systems, a personal computer facilitates the steps involved in tracking patients and obtaining highly customized analyses of the mammographic data base. The data in the mammographic data base exactly match those in the hospital's registration data and are easily transferred to other personal-computer programs for ancillary processing. CONCLUSION. This technique is ideal for departments that use a general-purpose radiology information system for mammographic reporting, yet need a more powerful but user-friendly and low-cost method for tracking their mammography patients.

Female↗

PubMed1990

Advances in materiel management systems technology.

When evaluating materiel management systems for your needs into the 1990s, be aware that the hardware you choose could be just as important as the software. It should 1) provide flexibility for growth, 2) provide access to a unified database for departments on-site as well as in remote locations, and 3) be easily managed and maintained by those that need it for critical day-to-day information. Software developers are already incorporating the new technologies in their programs and systems designs for the 1990s. Being up-to-date on the new hardware and new software will help you evaluate the right materiel management information system.

Catalogs, Commercial as Topic↗

PubMed1996

Maxsim, software for the analysis of multiple axonal arbors and their simulated activation.

In order to analyze the structural organization of complex axonal arbors reconstructed from histological serial sections, and to investigate the functional implications of their geometrical properties, we developed software providing the following facilities: (1) direct importation of data files generated by a commercially available 3-D light-microscopic reconstruction system, including routine procedures for identification and correction of data acquisition errors; (2) real-time 3-D rotations of the arbors in the stack of serial sections; (3) multiple interactive display modes; (4) possibility of modifying diameter and/or connectivity of different branches; (5) simulation of the invasion of the arbor by a single action potential initiated at any chosen point, and visualization of spatio-temporal profiles of activation; (6) extraction of quantitative data converted to standard file formats compatible with available mathematical software. All these tools can be applied to single or multiple axons, individually or simultaneously. The software, called Maxsim, is a highly flexible C-written program running on graphical workstations using the UNIX operating system and X-Window environment.

Animals↗

PubMed2003

[Three-dimensional-segmentation of the spine with specially adapted tools].

Segmented 3-D data of the spine form the basis for various modern clinical applications. Among these, multisegmental image fusion, image registration and finite element modeling for biomechanical analysis are promising innovative tools capable of facilitating treatment decisions and optimization of individual therapy in the future. However, the complex anatomy of the spine and the often extensive degenerative deformation presenting in clinical practice, generally limit the application of fully automated segmentation. A newly developed software system is presented that meets the complex requirements for image segmentation of the spine through the use of specially adapted interactive tools that take account of its axial skeletal structure. Furthermore, a standardized protocol is introduced that combines the newly developed interactive tools (rotation transformation, warped dissection plane) and standard segmentation tools to permit rapid and accurate segmentation. To date, the software environment presented herein has been applied with success to the segmentation of cervical, thoracic and lumbar spine.

Algorithms↗

PubMed2005

Software for automated application of a reference-based method for a posteriori determination of the effective radiographic imaging geometry.

OBJECTIVES: Presentation and validation of software developed for automated and accurate application of a reference-based algorithm (reference sphere method: RSM) inferring the effective imaging geometry from quantitative radiographic image analysis. METHODS: The software uses modern pattern recognition and computer vision algorithms adapted for the particular application of automated detection of the reference sphere shadows (ellipses) with subpixel accuracy. It applies the RSM algorithm to the shadows detected, thereby providing three-dimensional Cartesian coordinates of the spheres. If the three sphere centres do not lie on one line, they uniquely determine the imaging geometry. Accuracy of the computed coordinates is investigated in a set of 28 charge-coupled device (CCD)-based radiographs of two human mandible segments produced on an optical bench. Each specimen contained three reference spheres (two different radii r1=1.5 mm, r2=2.5 mm). True sphere coordinates were assessed with a manually operated calliper. Software accuracy was investigated for a weighted and unweighted algebraic ellipse-fitting algorithm. RESULTS: The critical depth- (z-) coordinates revealed mean absolute errors ranging between 1.1+/-0.7 mm (unweighted version; r=2.5 mm) and 1.4+/-1.4 mm (weighted version, r=2.5 mm), corresponding to mean relative errors between 5% and 6%. Outliers resulted from complete circular dense structure superimposition and one obviously deformed reference sphere. CONCLUSIONS: The software provides information fundamentally important for the image formation and geometric image registration, which is a crucial step for three-dimensional reconstruction from > or =2 two-dimensional views.

Algorithms↗

PubMed2004

[A new custom-made artificial articular cartilage of femoral condyle based on rapid prototyping technique: a case report].

OBJECTIVE: To design and manufacture a new custom-made artificial articular cartilage of femoral condyle based on rapid prototyping technique and explore a method to solve the necroses of allocartilage in hemi joint allotransplantation. METHODS: Design the new custom-made artificial articular cartilage of femoral condyle. The allograft and the patient distal femurs were scanned with Picker 6000 spiral computed tomography (CT) with 1.0 slice thickness and pitch of 1.5, reconstructed the distal femurs in Voxel Q image workstation with volume rendering technique. Then downloaded the transaxial 2D image data to personal computer at 0.1 mm interval and converted it into 2D digitized contour data by using image processing software developed by our team. The 3D wire frame and solid images of femoral condyle could be reconstructed when the 2D digitized contour data were input into image processing software Surfacer 9.0 (Imageware Company, USA). Subsequently based on the clinical experience and the need of design, the 3D contour image of articular cartilage was extracted from the surrounding. Based on the extracted 3D contour image, the computer-aided design (CAD) of the custom-made artificial articular cartilage was accomplished in Surfacer software, converted the CAD model into RP data format. Standard triangularization language, imported into the LPS600 rapid prototyping machine (Hengtong Company, Xi'an Jiaotong University, China), and the resin prototype was achieved. Then the resin model was used as a positive mould to build up a silica gel negative mould, the negative mould was sent to the factory to manufacture Ti-6Al-4V alloy articular cartilage through ordinary mould-melted founding process. Finally, the whole metal cartilage was completed after melting two special cages on it. A patient was selected to clinical applying. RESULTS: A new custom-made artificial articular cartilage of femoral condyle was made. It was press-fit well to the subchondral bone of the allograft bone. The patient's one and half year follow-up result was excellent. CONCLUSIONS: We design and manufacture a new custom-made artificial articular cartilage of femoral condyle based on rapid prototyping technique. The result shows that the manufacturing process has the advantage of rapidness and precision that are very important for individualized artificial implant manufacturing. The artificial articular cartilage is press-fit well and could be a good idea to solve the necroses of allocartilage in hemijoint allotransplantation.

Adolescent↗

PubMedDate not supplied

A simple method for the correction of distorted digital angiographic images for stereotactic target localization.

The most commonly used imaging modality for the diagnosis and localization of arteriovenous malformations (AVMs) treated with stereotactic radiotherapy is traditional angiography, but it would be desirable to also use digital subtraction angiography (DSA). However, DSA images are distorted due to the electron-optical characteristics of the X-ray image intensifier. For that reason, we have developed a method for the correction of the image distortion. The ISIS II Treatment Planning System (ISIS II TPS), developed at the Curie Institute, has been used for image acquisition and stereotactic localization. A grid phantom has been constructed for determining the distortion of the DSA images. The software developed for the correction has been implemented into the TPS and is based on a correction vector produced by matching the distorted and corrected grid points. The method has been tested for its ability to correct the position of all grid points as well as its effectiveness in real cases as compared to traditional angiography. The maximum displacement of the corrected grid points compared with their original position is measured to be 0.1 mm. The accuracy of the target localization using the corrected DSA images is comparable with traditional angiography localization and falls inside acceptable accuracy limits. In conclusion, this method offers the possibility of using DSA images for stereotactic localization without limiting the requested accuracy.

Angiography, Digital Subtraction↗

PubMed2006

A standard interface between simulation programs and systems analysis software.

A simple interface between simulation programs and systems analytical software is proposed. This interface is designed to facilitate linkage of environmental simulation programs with systems analytical software and thus can contribute to remedying the deficiency in applying systems analytical techniques to environmental modelling studies. The proposed concept, consisting of a text file interface combined with a batch mode simulation program call, is independent of model structure, operating system and programming language. It is open for implementation by academic and commercial simulation and systems analytical software developers and is very simple to implement. Its practicability is demonstrated by implementations for three environmental simulation packages (AQUASIM, SWAT and LEACHM) and two systems analytical program packages (UNCSIM, SUFI). The properties listed above and the demonstration of the ease of implementation of the approach are prerequisites for the stimulation of a widespread implementation of the proposed interface that would be beneficial for the dissemination of systems analytical techniques in the environmental and engineering sciences. Furthermore, such a development could stimulate the transfer of systems analytical techniques between different fields of application.

Environment↗

PubMedDate not supplied

Content preauthoring: preparing medical imaging information for multimedia authoring and quizzing.

Recent advances in multimedia development software and related hardware have given professionals and nonprofessionals tremendous power and flexibility to create multimedia education and training programs. Nevertheless, content organization remains a key and often neglected component of program development. Content preauthoring puts findings, diagnoses, differential diagnoses, and other standard radiologic concepts into a format that fosters logical program layout, centralized remediation, record keeping, decreased data entry, a variety of user levels, easy addition of cases, and linkage to a question-generating program. The goal of content preauthoring is to organize radiologic material into a hierarchical or spreadsheet-based structure that provides a logical basis for software design. By separating content design from software authoring, both processes become more manageable. This approach is applicable to visually oriented topics that focus on identification. The highly structured, goal-oriented nature of the method makes it particularly suitable for newcomers to multimedia authoring.

Authorship↗

PubMed2001

Development and application of a sorption data base for the performance assessment of a radwaste repository.

A sorption data base (SDB) provides readily available data for the performance assessment of a radwaste repository when site-specific and/or reference data are needed. The software developed at KAERI, SDB-21C, is a graphic user interface (GUI) program that provides efficient and user-friendly tools for evaluating large amount of sorption data. In addition, the most comprehensive sorption data base that contains about 11,000 NEA data and 2,000 KAERI data was compiled in the program. Besides the simple Kd approach, a parametric model and its compiled data sets are also included in the SDB-21C. In order to evaluate the versatility of SDB-21C, several applications were performed for relevant hypothetical situations.

Adsorption↗

PubMedDate not supplied

Computers in the intensive care unit: promises yet to be fulfilled.

Computers, whether disguised as microprocessor-controlled bedside devices or obvious as electronic patient charts, are proliferating in intensive care units. The history of the relationship between computers and intensive care units suggests that their joint development has been characterized by customization of a device or a program to automate each specific task. Failure to develop standard definitions of clinical data, standards for their interpretation, or a comprehensive model of the process of critical care retards development of computer systems beyond device-dedicated microprocessors. An agenda that gives priority to systematic examination of definitions, descriptions, and processes of critical care over additional hardware and software development is recommended.

Computer Systems↗

PubMed2006

An object-oriented programming system for the integration of internet-based bioinformatics resources.

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.

Computational Biology↗

PubMed1989

A cardiac potential mapping system.

The technical aspects of a multiple-purpose cardiac mapping system are presented. The authors begin with a brief history of hardware and software development and then concentrate on the major problems in acquiring high-quality recordings from the torso surface or from the epicardial surface and on the processing of the signals for display of color maps or other analysis. To achieve the desired adaptability to a variety of cardiac applications and experiments, they incorporated three parallel microprocessors that can record the signals from 240 electrodes and simultaneously provide display and analysis of the incoming cardiac data. While the parallel processors and modular software offer computational and flexibility advantages, the user interacts with an ordinary AT-compatible computer. This discussion is not a survey of the systems used in the many research laboratories or specific cardiac applications but is focused on experience in developing the specific hardware for such a multi-purpose instrument, and less specifically on the software that makes the system easy to use and adaptable to a variety of experimental and clinical situations.

Action Potentials↗

PubMed2002

Development of perfusion CT software for personal computers.

RATIONALE AND OBJECTIVES: The authors developed software for creating quantitative maps of arterial and portal perfusion in the upper abdominal organs on personal computers. The image quality of these perfusion computed tomographic (CT) images was visually evaluated. MATERIALS AND METHODS: In 58 patients (38 men, 20 women; mean age, 63.9 years +/- 11.9; range, 22-85 years) with various diseases of the upper abdomen, 91 single-section dynamic CT studies were obtained. The data were transferred on-line to a personal computer, and quantitative maps of arterial and portal perfusion were created by means of the maximum-slope method. Perfusion CT images were reviewed by a radiologist and a radiation technologist, and image quality was rated according to a four-category scoring system (1 = good quality, 2 = moderate, 3 = poor, 4 = images could not be created). RESULTS: Arterial perfusion CT images could be created in 81 (89%) of 91 examinations, and 74 images (81%) were scored as 1 or 2. Portal perfusion CT images could be created in 60 (68%) of 88 examinations, in which a portal trunk was included in the section, and 33 of them (38%) were scored as 1 or 2. Patient motion during dynamic CT sequences resulted in poor image quality in seven arterial and 27 portal perfusion images. CONCLUSION: Perfusion CT can combine quantitative perfusion maps with good anatomic detail in one image, although patient movement frequently degrades image quality in portal perfusion CT.

Abdomen↗

PubMedDate not supplied

Diet in the Italian EPIC cohorts: presentation of data and methodological issues.

One of the aims of the EPIC study is to produce accurate descriptions of the dietary habits of the participants recruited in the 27 EPIC centers of 10 European countries. To do this, different dietary assessment instruments were developed and applied to capture the wide range of diets characterizing the different European populations. Three different food frequency questionnaires were developed for Italy: one for the centers of Varese, Turin and Florence, one for Ragusa and one for Naples. These inquired about eating habits over the previous year and were completed by 46,839 Italian EPIC participants. Specially developed software analyzed the responses and linked them to food composition tables in order to provide a nutritional breakdown of individual and collective diets. A further aim of EPIC was to develop a method of rendering data from different dietary questionnaires comparable. To do this, dietary data were collected from a sample of about 8% of the Italian EPIC cohort, using a standardized computer-driven 24-hour dietary recall interview, and then compared with the dietary data collected by the questionnaires. This paper provides an extensive description of the technical features and performance of the food frequency questionnaires and the 24-hour recall interview, including a comparison of estimates of the intake of different food groups provided by the two instruments. From this comparison, the repeatability and reliability of consumption estimates was assessed, resulting in indications for improving data comparability. The paper also presents food frequency questionnaire estimates of the daily intake of foods and nutrients by center, sex and age group, as well as information on dietary habits such as place and time of intake, and food preparation and preservation methods as provided by the 24-hour recall interview. The picture that emerged is that Italian eating habits are undergoing marked changes, with a tendency to less healthy eating. Documentation of these changes in relation to age, sex and region provides an essential starting point for investigating the influence of diet on the development of cancer and other chronic diseases.

Age Distribution↗

PubMed2003

Epi info - present and future.

Epi Info is a suite of public domain computer programs for public health professionals developed by the Centers for Disease Control and Prevention (CDC). Epi Info is used for rapid questionnaire design, data entry and validation, data analysis including mapping and graphing, and creation of reports. Epi Info was originally created in 1985 using Turbo Pascal. In 1998, the last version of Epi Info for DOS, version 6, was released. Epi Info for DOS is currently supported by CDC but is no longer updated. The current version, Epi Info 2002, is Windows-based software developed using Microsoft Visual Basic. Approximately 300,000 downloads of Epi Info software occurred in 2002 from approximately 130 countries. These numbers make Epi Info probably one of the most widely distributed and used public domain programs in the world. The DOS version of Epi Info was translated into 13 languages, and efforts are underway to translate the Windows version into other major languages. Versions already exist for Spanish, French, Portuguese, Chinese, Japanese, and Arabic.

Centers for Disease Control and Prevention, U.S.↗