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PubMed2002

New computational approaches for analysis of cis-regulatory networks.

The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.

Chromosomes, Artificial, Bacterial↗

PubMed1986

The maintenance, distribution and development of biomedical computer software: an exercise in software engineering.

The growing reliance of biomedical investigations on computer software in almost all facets of their work places considerable emphasis on the need for the integrated management of the software. In order to efficiently develop, distribute, and maintain the software, tools are required which not only automate these tasks but also, wherever possible, 'semi-intelligently', alert their user to irregular situation. We describe an assortment of such tools routinely used in the management of the SAAM/CONSAM biokinetic software and illustrate their application. Furthermore, using these techniques we have presented some comparative performances of numerical integrators and of computer processors.

Computers↗

PubMed2005

Analysis of glioma cell platinum response by metacomparison of two-dimensional chromatographic proteome profiles.

Successful clinical development of cancer treatments is aided by the development of molecular markers that allow the identification of patients likely to respond. In the case of broadly cytotoxic drugs, such as the multinuclear series of platinum chemotherapeutic agents that we are evaluating for the treatment of glioma, one route to marker identification is proteomic profiling. We are using the two-dimensional chromatography system, the ProteomeLab PF2D, to compare proteomic profiles of glioma cells in culture before and after drug treatment. The existing software tools allowed the rapid identification of peaks increased by treatment of a given drug as compared with control untreated cells. To compare across these pairs, we developed new software, called the MetaComparison Tool (MCT). The MCT uses the chromatographic characteristics of peaks as identifiers, an approach that was validated by mass spectrometry of two independent isolations of a peak, from cells that were treated with two different platinum compounds. The MCT made it possible to rapidly query whether a given peak responded to more than one treatment and so allowed the identification of peaks that were specific to a given drug. As a result, this analysis greatly reduced the list of peaks whose isolation and downstream analysis by mass spectrometry is warranted, accelerating the search for protein markers of response.

Antineoplastic Agents↗

PubMed2005

T-Reg Comparator: an analysis tool for the comparison of position weight matrices.

T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position weight matrices. The user inputs a set of such weight matrices or binding site sequences and our program matches them against the T-Reg database, which is presently built on data from the Transfac [E. Wingender (2004) In Silico Biol., 4, 55-61] and Jaspar [A. Sandelin, W. Alkema, P. Engstrom, W. W. Wasserman and B. Lenhard (2004) Nucleic Acids Res., 32, D91-D94]. Our tool delivers a detailed report on similarities between user-supplied motifs and motifs in the database. Apart from simple one-to-one relationships, T-Reg Comparator is also able to detect similarities between submatrices. In addition, we provide a user interface to a program for sequence scanning with weight matrices. Typical areas of application for T-Reg Comparator are motif and regulatory module finding and annotation of regulatory genomic regions. T-Reg Comparator is available at http://treg.molgen.mpg.de.

Binding Sites↗

PubMed2004

Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data.

Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and customized datasets on linear chromosome maps constructed from annotated genome sequences. Genome2D facilitates the analysis of transcriptome data by using different color ranges to depict differences in gene-expression levels on a genome map. Such output format enables visual inspection of the transcriptome data, and will quickly reveal transcriptional units, without prior knowledge of expression level cutoff values. The compiled version of Genome2D is freely available for academic or non-profit use from http://molgen.biol.rug.nl/molgen/research/molgensoftware.php.

Bacterial Proteins↗

PubMed2004

Maximum pixel spectrum: a new tool for detecting and recovering rare, unanticipated features from spectrum image data cubes.

A new software tool, the maximum pixel spectrum, detects rare events within a spectrum image data cube, such as that generated with electron-excited energy-dispersive X-ray spectrometry in a scanning electron microscope. The maximum pixel spectrum is a member of a class of 'derived spectra' that are constructed from the spectrum image data cube. Similar to a conventional spectrum, a derived spectrum is a linear array of intensity vs. channel index that corresponds to photon energy. A derived spectrum has the principal characteristics of a real spectrum so that X-ray peaks can be recognized. A common example of a derived spectrum is the summation spectrum, which is a linear array in which the summation of all pixels within each energy plane gives the intensity value for that channel. The summation spectrum is sensitive to the dominant features of the data cube. The maximum pixel spectrum is constructed by selecting the maximum pixel value within each X-ray energy plane, ignoring the remaining pixels. Peaks corresponding to highly localized trace constituents or foreign contaminants, even those that are confined to one pixel of the image, can be seen at a glance when the maximum pixel spectrum is compared with the summation spectrum.

Aluminum↗

PubMed2026

ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data.

MOTIVATION: Chemical genomics is a powerful high-throughput approach to systematically link phenotypes to genotypes. However, the vast datasets generated remain challenging to explore due to the lack of integrated, interactive tools for visualization and analysis. Existing workflows often require multiple independent software tools, limiting data accessibility and collaboration. Therefore, we created a user-friendly platform that enables efficient exploration and sharing of chemical genomics data. RESULTS: We developed ChemGenXplore, a web-based Shiny application designed to streamline the visualization and analysis of chemical genomic screens. It offers two primary functionalities: one for exploring pre-implemented datasets and another for analysing user-uploaded datasets. ChemGenXplore enables users to visualize phenotypic profiles, assess gene-gene and condition-condition correlations, perform GO and KEGG enrichment analysis, and generate customizable, interactive heatmaps. To further support collaborative research, ChemGenXplore also facilitates the comparative analysis of chemical genomic and other omics datasets. By consolidating these features into a single interactive and accessible tool, ChemGenXplore facilitates data sharing, enhances reproducibility, and promotes collaboration within the research community. AVAILABILITY AND IMPLEMENTATION: ChemGenXplore is freely accessible as a web application at https://chemgenxplore.kaust.edu.sa/. Source code and documentation, including instructions for local installation, are provided on GitHub (https://github.com/Hudaahmadd/ChemGenXplore). A Docker image is also available on DockerHub (https://hub.docker.com/r/hudaahmad/chemgenxplore) to ensure reproducibility and simplify installation.

Software↗

PubMed2005

Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection.

BACKGROUND: The extraction of biological knowledge from genome-scale data sets requires its analysis in the context of additional biological information. The importance of integrating experimental data sets with molecular interaction networks has been recognized and applied to the study of model organisms, but its systematic application to the study of human disease has lagged behind due to the lack of tools for performing such integration. RESULTS: We have developed techniques and software tools for simplifying and streamlining the process of integration of diverse experimental data types in molecular networks, as well as for the analysis of these networks. We applied these techniques to extract, from genomic expression data from Hepatitis C virus-infected liver tissue, potentially useful hypotheses related to the onset of this disease. Our integration of the expression data with large-scale molecular interaction networks and subsequent analyses identified molecular pathways that appear to be induced or repressed in the response to Hepatitis C viral infection. CONCLUSION: The methods and tools we have implemented allow for the efficient dynamic integration and analysis of diverse data in a major human disease system. This integrated data set in turn enabled simple analyses to yield hypotheses related to the response to Hepatitis C viral infection.

Computational Biology↗

PubMed2006

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge.

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.

Biomedical Research↗

PubMed2003

A new approach to PLC software design.

This paper presents a model-based approach to PLC software development. The essence of this approach is the introduction of a new procedural modeling language called ProcGraph. In contrast to commonly used methods, ProcGraph deals with the procedural aspect of the control system and allows software specification at a higher level of abstraction. The modeling language has been supported with the development of a software tool which facilitates graphical model design and automatic code generation. The specification notation has been tested in the development of software for industrial applications. The supporting tool has been tested in a laboratory environment.

Journal Article↗

PubMed2002

BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.

MOTIVATION: Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet. RESULTS: We present a new software system--BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model--BioCore--which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms. AVAILABILITY: http://www.zbi.uni-saarland.de/chair/projects/BioMiner SUPPLEMENTARY INFORMATION: Additional information on experimental results can be found on our web site.

Biochemistry↗

PubMed2004

SPRINT: a tool for probabilistic source term prediction for use with decision support systems.

This paper describes a software tool, SPRINT, that has been developed within the FP5 STERPS project for rapid source term prediction. It is based entirely on a probabilistic approach to the diagnosis and prognosis of Nuclear Power Plant status, based on key instrument readings and other observations. In principle, the method can be applied to any accident sequence from the benign to the most severe. However, the main benefits are seen for the diagnosis of plant status during degraded core conditions where the accident phenomenology is either uncertain or essentially non-deterministic in nature. The output from SPRINT consists of a set of potential source terms with an estimate of the likelihood of each.

Computer Simulation↗

PubMed2002

FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification.

FindPept (http://www.expasy.org/tools/findpept.html) is a software tool designed to identify the origin of peptide masses obtained by peptide mass fingerprinting which are not matched by existing protein identification tools. It identifies masses resulting from unspecific proteolytic cleavage, missed cleavage, protease autolysis or keratin contaminants. It also takes into account post-translational modifications derived from the annotation of the SWISS-PROT database or supplied by the user, and chemical modifications of peptides. Based on a number of experimental examples, we show that the commonly held rules for the specificity of tryptic cleavage are an oversimplification, mainly because of effects of neighboring residues, experimental conditions, and contaminants present in the enzyme sample.

Algorithms↗

PubMed2005

A simulation tool to support teaching and learning the operation of X-ray imaging systems.

We present a software tool for the simulation of an X-ray imaging systems. It consists of three virtual objects: the X-ray source, the human body and the detector. The X-ray source is modeled as a radiological tube for which the user can modify the tube potential, the anode material, the tube load, the filtration and some geometric parameters, such as source-skin distance, orientation and field size. The virtual body consists of a 3D voxel matrix in which CT numbers for each point of the body are stored, obtained from tomographic slices. The interactions of X-rays passing through the body are evaluated using pencil beam technique. The image is obtained computing the dose absorbed by the detector and converting it into optical density by the use of a proper response function. The dose absorbed in each point of the body is also computed and can be visualized both in 2D and 3D representations. The influence of each parameter on the beam spectrum, on the image quality and on the dose to the patient can be observed interactively.

Biomedical Engineering↗

PubMed1986

Design, development, and implementation of a data processing system for multiple controlled trials and epidemiologic studies.

We were given the opportunity to design and implement a general data processing system to accommodate several different epidemiologic studies to be conducted by a new research group. A survey of 15 operating data centers was conducted in preparation for undertaking the design and development of our system. The results of the survey indicated that data processing activities can be classified, both conceptually and operationally, into three modules: data recording and data entry, data management, and data analysis, and that the data management functions were those amenable to generalization. Based on our survey and the varying needs of our studies, we selected a "mixed" hardware environment, using both a computer center mainframe and microcomputers. We created the systems using commercially available software, including a mainframe database manager and mainframe statistics packages, microcomputer data entry software, and a communications package to link the two environments. Our strategy was to buy software, when possible, rather than to build custom programs, and to let software tools govern hardware needs. Hardware independence, price, and functional capability directed our software choices, while hardware selection was constrained most importantly by available software, then by budget, by available computing resources, and finally by the marketplace. The system has been used successfully in three studies differing in design, size, data collection locale, and rate of data accrual.

Data Collection↗

PubMed1997

Designing Radiotherapy Software Components and Systems That Will Work Together.

The radiation treatment planning and delivery process requires that many different computerized data sources, software tools, and computer control systems be smoothly integrated. These include computer-controlled accelerators and new digital imaging modalities. At the same time, the applications themselves are becoming increasingly complex. In radiotherapy, the variety of components to integrate is much greater than in other areas of clinical medicine, growing out of more than a 30-year history of use of highly stylized traditional computer applications and many rigid conventions and practices associated with these computer programs. The introduction of new tools and computer-controlled equipment influenced the evolution of radiotherapy planning software, leading us to take a new look at how radiotherapy planning is done. Addressing and solving these integration problems as a serious research undertaking is vital to continued success in deploying computer applications for clinical use. New software design ideas such as object oriented design, behavioral abstraction and mediators can solve these problems. Our experience shows that the time and effort to build high-quality adaptable modular systems can be kept modest and within the reach of a small development team.

Journal Article↗

PubMed2001

GALEN ten years on: tasks and supporting tools.

The GALEN technology has matured over more than a decade of use. We describe a set of software tools and associated methodologies that together are supporting ontological engineering in a production, rather than a research setting.

Artificial Intelligence↗

PubMed2005

Integrating information technologies as tools for surgical research.

BACKGROUND: Surgical research is dependent upon information technologies. Selection of the computer, operating system, and software tool that best support the surgical investigator's needs requires careful planning before research commences. MATERIALS AND METHODS: This manuscript presents a brief tutorial on how surgical investigators can best select these information technologies, with comparisons and recommendations between existing systems, software, and solutions. RESULTS: Privacy concerns, based upon HIPAA and other regulations, now require careful proactive attention to avoid legal penalties, civil litigation, and financial loss. Security issues are included as part of the discussions related to selection and application of information technology. CONCLUSIONS: This material was derived from a segment of the Association for Academic Surgery's Fundamentals of Surgical Research course.

Biomedical Research↗