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At least 1,207 records · Page 67Linked to original sources
PubMed2006

PIANA: protein interactions and network analysis.

UNLABELLED: We present a software framework and tool called Protein Interactions And Network Analysis (PIANA) that facilitates working with protein interaction networks by (1) integrating data from multiple sources, (2) providing a library that handles graph-related tasks and (3) automating the analysis of protein-protein interaction networks. PIANA can also be used as a stand-alone application to create protein interaction networks and perform tasks such as predicting protein interactions and helping to identify spots in a 2D electrophoresis gel. AVAILABILITY: PIANA is under the GNU GPL. Source code, database and detailed documentation may be freely downloaded from http://sbi.imim.es/piana.

Computer Graphics↗
PubMed2026

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.

Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We develop a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implement it in the SuPreMo-Akita software. With this tool, we rank hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This reveals that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritize candidate variants that disrupt ASD CREints and validate our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study suggests that disrupted genome folding is a potential genetic mechanism in a subset of ASD cases and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.

Humans↗
PubMed1991

The application of SSADM to modelling the logical structure of proteins.

A logical design that describes the overall structure of proteins, together with a more detailed design describing secondary and some supersecondary structures, has been constructed using the computer-aided software engineering (CASE) tool, Auto-mate. Auto-mate embodies the philosophy of the Structured Systems Analysis and Design Method (SSADM) which enables the logical design of computer systems. Our design will facilitate the building of large information systems, such as databases and knowledgebases in the field of protein structure, by the derivation of system requirements from our logical model prior to producing the final physical system. In addition, the study has highlighted the ease of employing SSADM as a formalism in which to conduct the transferral of concepts from an expert into a design for a knowledge-based system that can be implemented on a computer (the knowledge-engineering exercise). It has been demonstrated how SSADM techniques may be extended for the purpose of modelling the constituent Prolog rules. This facilitates the integration of the logical system design model with the derived knowledge-based system.

Amino Acid Sequence↗
PubMed2005

Atlas - a data warehouse for integrative bioinformatics.

BACKGROUND: We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. DESCRIPTION: The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. CONCLUSION: The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

Computational Biology↗
PubMed2005

Graphical representation of ribosomal RNA probe accessibility data using ARB software package.

BACKGROUND: Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. RESULTS: The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence associated information (SAI) can be visualized by user defined background colors within the ARB primary and secondary structure editors as well as in the PROBE Match tool. CONCLUSION: Using this tool, in silico probe design and evaluation can be performed with respect to in situ probe accessibility data. The evaluation of proposed probe targets with respect to higher-order rRNA structure is of importance for successful design and performance of in situ hybridization experiments. The entire ARB software package along with the probe accessibility data is available from the ARB home page http://www.arb-home.de

Algorithms↗
PubMed1989

A programmable system for acquisition and reduction of respiratory physiological data.

A portable software package (TIDAL--Tools for Intelligent Data Acquisition in the Laboratory) for acquiring and analyzing respiratory physiological data is described. TIDAL supports flow-, volume-, and concentration-measuring devices, and any other instruments that produce linear analog outputs. The system allows users to specify the names and types of channels to be sampled, and the calculations involved in reducing samples to breath-to-breath values. The specification of channels and calculations is given in EDL, an Experiment Description Language designed for respiratory physiology. EDL comprises a set of internal functions (primitives) which can be combined into arbitrarily complex expressions. To simplify EDL programming, TIDAL includes a macro processor and a standard macro library; the library contains definitions for a wide variety of respiratory variables. Examples are inspiratory and expiratory times and total volumes, mean inspired and expired gas volumes and concentrations, and end-tidal concentrations. Variables that are derived from these primary data, such as respiratory quotient, are also easily specified. TIDAL is written entirely in the C programming language, with special attention to portable coding practices. The code is organized in a modular structure that eases porting to multiple hardware/compiler/operating system environments.

Expert Systems↗
PubMed2006

Analysis of a mammography teaching program based on an affordance design model.

RATIONALE AND OBJECTIVES: The wide use of computer technology in education, particularly in mammogram reading, asks for e-learning evaluation. The existing media comparative studies, learner attitude evaluations, and performance tests are problematic. Based on an affordance design model, this study examined an existing e-learning program on mammogram reading. MATERIALS AND METHODS: The selection criteria include content relatedness, representativeness, e-learning orientation, image quality, program completeness, and accessibility. A case study was conducted to examine the affordance features, functions, and presentations of the selected software. Data collection and analysis methods include interviews, protocol-based document analysis, and usability tests and inspection. Also some statistics were calculated. RESULTS: The examination of PBE identified that this educational software designed and programmed some tools. The learner can use these tools in the process of optimizing displays, scanning images, comparing different projections, marking the region of interests, constructing a descriptive report, assessing one's learning outcomes, and comparing one's decisions with the experts' decisions. Further, PBE provides some resources for the learner to construct one's knowledge and skills, including a categorized image library, a term-searching function, and some teaching links. Besides, users found it easy to navigate and carry out tasks. The users also reacted positively toward PBE's navigation system, instructional aids, layout, pace and flow of information, graphics, and other presentation design. CONCLUSION: The software provides learners with some cognitive tools, supporting their perceptual problem-solving processes and extending their capabilities. Learners can internalize the mental models in mammogram reading through multiple perceptual triangulations, sensitization of related features, semantic description of mammogram findings, and expert-guided semantic report construction. The design of these cognitive tools and the software interface matches the findings and principles in human learning and instructional design. Working with PBE's case-based simulations and categorized gallery, learners can enrich and transfer their experience to their jobs.

Breast Neoplasms↗
PubMed2003

New cancer biomarkers deriving from NCI early detection research.

Cancer is not a single disease but an accumulation of several events, genetic and epigenetic, arising in a single cell over a long time interval. A high priority in the cancer field is to identify these events. This can be achieved by characterizing cancer-associated genes and their protein products. Identifying the molecular alterations that distinguish any particular cancer cell from a normal cell will ultimately help to define the nature and predict the pathologic behavior of that cancer cell. It will also indicate the responsiveness to treatment of that particular tumor. Understanding the profile of molecular changes in any particular cancer will be extremely useful as it will become possible to correlate the resulting phenotype of that cancer with molecular events. Achieving these goals and knowledge will provide an opportunity for discovering new biomarkers for early cancer detection and developing prevention approaches. This will also help us identify new targets for therapeutic development. Advancement in technology includes methods and tools that enable research including, but not limited to, instrumentation, techniques, devices, and analysis tools (e.g., computer software). Resources such as databases, reagents, and tissue repositories are different than technologies. The identification and definition of the molecular profiles of cancer will require the development and dissemination of high-throughput molecular analysis technologies, as well as elucidation of all of the molecular species embedded in the genome of cancer and normal cells. The main challenge in cancer control and prevention is to detect the cancer early. This could then enable effective interventions and therapies contributing to reduction in mortality and morbidity. At a specific time, biomarkers serve as molecular signposts of the physiologic state of a cell. These signposts are the result of genes, their products (proteins) and other organic chemicals made by the cell. Biomarkers could prove to be vital for the identification of early cancer and subjects at risk of developing cancer as a normal cell progresses through the complex process of transformation to a cancerous state. This chapter discusses ongoing research in genetic and proteomic approaches to identify molecular signatures such as protein profiles, microsatellite instability, hypermethylation, and single nucleotide polymorphisms. Other topics covered here include the use of genomics and proteomics as high-throughput technology platforms to facilitate biomarker-aided detection of early cancer. Other areas covered include issues surrounding the analysis, validation, and predictive value of biomarkers using such technologies. Recent advances in noninvasive techniques, such as buccal cell isolates serving as viable sources of biomarkers, complementary to traditional sources such as serum or plasma, are also presented. The review also brings attention to the efforts of the Early Detection Research Network (EDRN) at the National Cancer Institute (NCI), in bringing together scientific expertise from leading national and international institutions, to identify and validate biomarkers for the detection of precancerous and cancerous cells in determining risk for developing cancer. The network's serious determined efforts in linking discovery to process development, resulting in early detection tests and clinical assessment, are also discussed.

Biomarkers, Tumor↗
PubMed2005

Building medical ontologies by terminology extraction from texts: an experiment for the intensive care units.

In many medical fields, maintenance, comparison and aggregation of unambiguous terminologies go through formal specialized clinical terminologies: ontologies. We describe a methodology to build medical ontology from textual reports using a natural language processing tool, the SYNTEX software. The methodology is illustrated in the surgical intensive care medical domain. We have tested the possibility for an expert to build a sizeable ontology in a reasonable time. The quality of the ontology has been evaluated according to its capacity to cover the ICD-10 terminology in the field. Finally, the methodology itself is discussed.

Humans↗
PubMed2003

Quantitative cytokine gene expression in human tonsils at excision and during histoculture assessed by standardized and calibrated real-time PCR and novel data processing.

Real-time reverse transcription polymerase chain reaction (RT-PCR) assays were developed for the quantification of expression of the genes for human interleukin (IL)-1beta, IL-2, IL-6, IL-8, IL-10, IL-12, IL-15, interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, transforming growth factor (TGF)-beta and for the endogenous reference hydroxymethylbilane synthase (HMBS). The assays detected as little as five plasmid copies and were 100% specific. The creation and integration of a calibration sample into the assays permitted their calibration across experiments. To handle the high number of generated data, the correlator of advanced real-time assays (CARTA) software was designed to organize samples and to automatically control and analyze TaqMan real-time RT-PCR data. The RT-PCR assays were applied to quantify levels of cytokine gene expression in human palatine tonsils at excision and during 4 days of histoculture. Similar longitudinal patterns of cytokine gene expression were observed in all donors, but the variations in spontaneous expression levels between donors were large. The expression levels in histocultures were constant over time and similar to the expression levels at excision except for IL-6 and IL-8, which markedly increased following the first 24 h of culture, possibly due to the initial stress. The standardized and calibrated RT-PCR assays quantify gene expression of human cytokines proved sensitive and specific for the investigation of cell behavior at the molecular level and the newly established CARTA software, a reliable tool for rapid data handling. Tonsil histocultures could serve as a valuable ex vivo model system for further, donor-dependent, studies on activation or repression of cytokine gene expression.

Calibration↗
PubMed1997

Potential of high-performance liquid chromatography with photodiode array detection in forensic toxicology.

The potentials and limitations of high-performance liquid chromatography-photodiode array detection are highlighted in respect to its use in the analysis of different biological matrices followed by the identification of unknowns. The logical analytical approach used in clinical and forensic toxicology, vital for the identification of one or more toxic substances as a cause of intoxication, is largely based on both simple and fast "general unknown screening" methods which cover most relevant drugs and potentially hazardous chemicals. In this field of systematic toxicological analysis, a literature overview shows that HPLC can play a substantial role. Both column packing material and eluent composition have their impact on intra- and interlaboratory reproducibility. In view of the sometimes different retention characteristics of various HPLC columns, several possibilities are addressed to enhance the discriminating power of primary retention parameters. The advantages of photodiode array detection as compared to UV detection have been of paramount importance to the success of HPLC in toxicological analysis. Dedicated libraries with spectral information and searching software are powerful tools in the process of identification of an unknown substance. In the present paper, these aspects are also verified in a number of real cases, i.e., trazodone and dothiepin, azide, chloroquine and cocaine, in which we illustrate from our own experience the potentials of HPLC-photodiode array detection in systematic toxicological analysis.

Adult↗
PubMed2001

Statistical inference of sequence-dependent mutation rates.

Several lines of research are now converging towards an integrated understanding of mutational mechanisms and their evolutionary implications. Experimentally, crystal structures reveal the effect of sequence context on polymerase fidelity; large-scale sequencing projects generate vast amounts of sequence polymorphism data; and locus-specific databases are being constructed. Computationally, software and analytical tools have been developed to analyze mutational data, to identify mutational hot spots, and to compare the signatures of mutagenic agents.

Computational Biology↗
PubMed1997

Benefits of an electronic clinical information system: an intensive care nursing perspective.

Due to advancements in surgery, medicine and equipment, the modern intensive care unit (ICU) patient necessitates the recording of vast amounts of data. The management of these data is increasingly impinging on nursing time. A review of the literature describes the potential benefits of using a clinical information system (CIS) to record and save data electronically rather than transcribing it onto conventional charts. Commercial systems that can perform these tasks are available but have severe financial implications in terms of initial costs, maintenance and upgrading. Work is continuing at Killingbeck Hospital on a project developing and introducing a CIS into intensive care using standard hardware, software and programming tools thus minimizing these costs.

Budgets↗
PubMedDate not supplied

Low-resolution gamma-ray measurements of process hold-up.

This tool, consisting of software with a compact detector, an M3CA, and an Intermec datalogger: 1. acquires and manages several hundred spectra in an hour; 2. produces prompt and reliable quantitative analyses; 3. is self-powered, easily carried and operated by a single user; 4. accomodates varying degrees of user expertise; 5. corrects for the effects of equipment geometry; 6. corrects for the effects of equipment attenuation; 7. tolerates facility variables such as temperature fluctuations and equipment accessibility; 8. has been subjected to quality testing under field conditions; and 9. does not require extensive specialized training for the operators.

Calibration↗
PubMed2002

MOSBY: a molecular structure viewer program with portability and extensibility.

A molecular structure viewer program, MOSBY has been developed for studies that use atomic coordinates to understand the structures of protein molecules. The program is designed to be portable with a comprehensive user interface by our high-throughput graphics library. In addition, it cooperates with extension modules customized for individual research topics and analysis. For example, an electron density module loads and displays electron density maps derived in X-ray crystallographic analysis superimposed to an atomic model. A molecular dynamics module reads a trajectory file of the results of molecular dynamics calculations and animates the structure. These plug-in modules are devised to function without modification to the MOSBY program. For variations of analysis and calculations with atomic coordinates, the portability and extensibility illustrated by MOSBY play an important rule in scientific computational tools with active software development.

Computer Graphics↗
PubMed2005

Targeted comparative proteomics by liquid chromatography-tandem Fourier ion cyclotron resonance mass spectrometry.

In proteomics, effective methods are needed for identifying the relatively limited subset of proteins displaying significant changes in abundance between two samples. One way to accomplish this task is to target for identification by MS/MS only the "interesting" proteins based on the abundance ratio of isotopically labeled pairs of peptides. We have developed the software and hardware tools for online LC-FTICR MS/MS studies in which a set of initially unidentified peptides from a proteome analysis can be selected for identification based on their distinctive changes in abundance following a "perturbation". We report here the validation of this method using a mixture of standard proteins combined in different ratios after isotopic labeling. We also demonstrate the application of this method to the identification of Shewanella oneidensis peptides/proteins exhibiting differential abundance in suboxic versus aerobic cell cultures.

Bacterial Proteins↗
PubMedDate not supplied

Cage: software for a critical analysis of (2)H spin-lattice relaxation in liquid crystals.

A software package of Mathematica, aimed at the analysis of (2)H NMR Zeeman (T(1Z)) and quadrupolar (T(1Q)) spin-lattice relaxation times in liquid crystals in terms of diffusional models, is presented. The models most commonly used to describe internal, overall, and collective motions in liquid-crystalline phases are considered, and dynamic parameters are obtained by means of either single point or global target approaches using simulation or fitting procedures. The use of the software as a tool for highlighting the problems encountered in this kind of analysis as well as for dealing with such problems following suitable strategies is illustrated by means of applications to experimental (2)H relaxation times of three different calamitic liquid crystals.

Journal Article↗
PubMed2001

Towards a Statewide Cardiac Surgery Database: the Victorian initiative.

The establishment of the Australasian Society of Cardiac and Thoracic Surgeons (ASCTS) at the beginning of the 1990s gave rise to an early proposal for the development of a cardiac surgical database. The Victorian Government gave its in-principle backing to a statewide database project from late 1997. Release of a promised dollar 200,000 grant for development was contingent on the ASCTS being able to fulfil several initial requirements. These were: (i) the provision of an indicative annual report outlining performance against a series of clinical indicators; (ii) an indicative peer-review process; and (iii) the addressing of issues surrounding intellectual property and ownership of any database that was developed. In outlining a strategy to be used in developing and implementing the project plan, it was determined by the project development team that all Victorian cardiac surgical units were, in fact, collecting similar data, but were using different software and analytical tools. The Cardiovascular Disease Prevention Unit at the Baker Medical Research Institute in Melbourne has developed a model of mortality and risk-adjusted complications out of the pooled Victorian data. This, it is hoped, will be a forerunner of a major achievement in the monitoring of cardiac surgery procedures nationally, and the attainment of national and international best practice.

Journal Article↗