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PubMed1987

Computer software for specimen orientation adjustment using double-tilt or rotation holders.

Computer software for specimen orientation adjustment relative to the incident electron beam has been developed. The difficulties encountered when tilting severely strained, highly beam-sensitive, or small-grain-size specimens with known structures using either a double-tilt or a rotation holder in transmission electron microscopy (TEM) can be minimized. Combined with computer programs for obtaining the reduced bases from diffraction patterns, the software is also useful for unknown crystals. The algorithm is introduced and examples are given.

Crystallization↗

PubMed1993

Software for quantitative immunogold and in situ hybridization.

A well-deserved criticism of stereology is that it is often too difficult to understand and use. Nevertheless, it is rapidly becoming one of the most effective ways of collecting and interpreting structural data in experimental biology. Recent breakthroughs in theory have produced a remarkable set of tools that can be used to engineer new methods. The dilemma remains, however, in that some of these new methods continue to be too difficult to understand and use. One solution to this growing problem of technology transfer might be to simplify the methods with computer software. To test this idea, programs were written for quantitative immunogold and in situ hybridization. Simulators were used to develop and test new experimental designs, which, in turn, were translated into step-by-step laboratory tool kits. This paper shows how these tool kits can turn two-dimensional section data into estimates for the number of labeled molecules in three-dimensional organelles, cells, tissues, and organs. The results indicate that software can identify the key data of an experiment and reduce the computational requirements of a new stereological method to entering constants and variables into data entry forms.

Animals↗

PubMed2005

Numerical approaches for quantitative analysis of two-dimensional maps: a review of commercial software and home-made systems.

The present review attempts to cover a number of methods that have appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this review to conventional two-dimensional (2-D) map analysis which couples orthogonally a charge-based step (isoelectric focusing) to a size-based separation step (sodium dodecyl sulfate-electrophoresis). The first and oldest method applied to 2-D map data reduction is based on statistical analysis performed on sets of gels via powerful software packages, such as Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately running a number of replicas for control and treated samples. The two sets of data are then merged and compared via a number of software packages which we describe. In addition to commercially-available systems, a number of home made approaches for 2-D map comparison have been recently described and are also reviewed. They are based on fuzzyfication of the digitized 2-D gel image coupled to linear discriminant analysis, three-way principal component analysis or a combination of principal component analysis and soft-independent modeling of class analogy. These statistical tools appear to perform well in differential proteomic studies.

Cluster Analysis↗

PubMed2005

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments.

The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR Pulsar quadrupole-TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.

Algorithms↗

PubMed2006

Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data.

The study of changes in protein levels between samples derived from cells representing different biological conditions is a key to the understanding of cellular function. There are two main methods available that allow both for global scanning for significantly varying proteins and targeted profiling of proteins of interest. One method is based on 2-D gel electrophoresis and image analysis of labelled proteins. The other method is based on LC-MS/MS analysis of either unlabelled peptides or peptides derived from isotopically labelled proteins or peptides. In this study, the non-labelling approach was used involving a new software, DeCyder MS Differential Analysis Software (DeCyder MS) intended for automated detection and relative quantitation of unlabelled peptides in LC-MS/MS data. Total protein extracts of E. coli strains expressing varying levels of dihydrofolate reductase and integron integrase were digested with trypsin and analyzed using a nanoscale liquid chromatography system, Ettan MDLC, online connected to an LTQTM linear ion-trap mass spectrometer fitted with a nanospray interface. Acquired MS data were subjected to DeCyder MS analysis where 2-D representations of the peptide patterns from individual LC-MS/MS analyses were matched and compared. This approach to unlabelled quantitative analysis of the E. coli proteome resulted in relative protein abundances that were in good agreement with results obtained from traditional methods for measuring protein levels.

Amino Acid Sequence↗

PubMed2006

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Amino Acid Sequence↗

PubMed2002

Software algorithm for automatic interpretation of mass spectra of glycerolipids.

A new software algorithm for automatic interpretation of mass spectra of glycerolipids has been developed. The algorithm utilizes a user-specified list of parameters needed to process the spectra. The compounds in mass spectra are identified according to range of measured m/z values, after which the spectra are automatically corrected by the content of naturally occurring isotopes and ion intensities of identified compounds by response correction factors. Automatic processing of the spectra was shown to be accurate and reliable by testing with numerous spectra of glycerophospholipids obtained by liquid chromatography/electrospray ionization mass spectrometry and by comparing the results with manual interpretation of the spectra. If quantitative analysis using internal standards is performed, all the identified compounds in the sample are quantified automatically. A dilution factor may be defined for each sample and is applied to correct the alterations in sample concentration during sample preparation. Processing of several replicate spectra simultaneously produces mean results with standard deviations. The software may also be used to subtract the results of two analyses and to calculate the mean result of replicate subtractions. The algorithm was shown to save time and labor in repetitive processing of mass spectra of similar type. It may be applied to processing of spectra obtained by various mass spectrometric methods.

Algorithms↗

PubMedDate not supplied

Software acceleration techniques for the simulation of scanning electron microscope images.

A scanning electron microscope (SEM) simulator was developed based on the models used in the MONSEL software. This simulator extends earlier work by introducing an object-oriented framework and adding optimization methods based on precomputation of electron trajectories. Several optimizations enable speedup by factors of 5-100 on a single processor over unoptimized simulations without introducing additional approximations. The speedup for a particular surface depends on the self-similarity of the surface at the scale of the electron penetration depth. We further accelerate by parallelizing the calculations for a total speedup of about 100-2000 on 30 processors. The goal of this work was to create a system capable of simulating a quantitatively accurate SEM image of a relatively unconstrained surface. Results of this work include simulation software, optimization algorithms, performance measurements with various optimizations, and examples of simulated images.

Algorithms↗

PubMedDate not supplied

Use of a desktop scanner and spreadsheet software for mapping arterial disease.

Mapping the surface area and distribution of atherosclerosis has so far required photographic, video, or photomicrographic imaging of the inner surface of the arterial wall, as well as laborious manual or sophisticated image processing methods of quantification. We investigated whether comparable results could be obtained by using a conventional flatbed scanner and readily available spreadsheet software. Lipid-rich lesions near 21 aortic branches from cholesterol-fed rabbits were mapped using a scanner-based technique and an established photomicrographic technique. When the tissue was counterstained and held on the scanner by a transparent weight to obtain adequate contrast and prevent detection of adventitial staining, the areas of lipid deposition detected by the two methods correlated highly (R2 = 0.99). Discrepancies arose mainly at the edges of lesions, probably because of alignment errors and better flattening of the tissue on the scanner; when these were accounted for, discrepancies occurred in < 1% of the total area examined. The new method produces results comparable with previous procedures, but is much more rapid and requires only office equipment and software.

Animals↗

PubMed1993

An evaluation of five commercial immunoassay data analysis software systems.

An evaluation of five commercial software systems used for immunoassay data analysis revealed numerous deficiencies. Often, the utility of statistical output was compromised by poor documentation. Several data sets were run through each system using a four-parameter calibration function, and the results were compared to those from an independent method. Comparable results between systems were obtained, but often several attempts at analysis were necessary. The evaluation process revealed that it is difficult to monitor the numerous options available on these types of programs, and that incorrect results could easily be obtained if comparison analyses were not used. Recommendations for improved software functionality and for using the four-parameter calibration model are presented.

Data Interpretation, Statistical↗

PubMed2002

Measurement of Ca2+-binding constants of proteins and presentation of the CaLigator software.

The complexity of Ca2+ cell signaling is dependent on a plethoria of Ca2+-binding proteins that respond to signals in different ranges of Ca2+ concentrations. Since the function of these proteins is directly coupled to their Ca2+-binding properties, there is a need for accurately determined equilibrium Ca2+-binding constants. In this work we outline the experimental techniques available to determine Ca2+-binding constants in proteins, derive the models used to describe the binding, and present CaLigator, software for least-square fitting directly to the measured quantity. The use of the software is illustrated for Ca2+-binding data obtained for two deamidated forms of calbindin D(9k), either an isospartate-56 (beta form) or a normal Asp-56 (alpha form). Here, the Ca2+-binding properties of the two isoforms have been studied using the chelator method. The alpha form shows similar Ca2+-binding properties to the wild type while the beta form has lost both cooperativety and affinity.

Calcium↗

PubMed1995

Software trapping: a strategy for finding genes in large genomic regions.

We present an approach to the gene identification phase of positional cloning that combines sparse sampling of DNA sequences from large genomic regions with computational analysis. We call the method "software trapping." The goal is to find coding exons while avoiding massive DNA sequence determination and contig assembly. Instead, rapid sequence sampling is combined with exon screening software such as a newly developed package called XPOUND to identify coding sequences. We have tested the approach using a set of model genomic sequences with known intron/exon structures as well as with bona fide P1 genomic clones. The results suggest that the strategy is a useful complement to other methods for finding genes in poorly characterized regions of genomes.

Bacteriophage P1↗

PubMed1994

The genome reconstruction manager: a software environment for supporting high-throughput DNA sequencing.

A new software system designed for use in high-throughput DNA sequencing laboratories is described. The Genome Reconstruction Manager (GRM) was developed from requirements derived from ongoing large-scale DNA sequencing projects. Object-oriented principles were followed in designing the system, and tools supporting object-oriented system development were employed for its implementation. GRM provides several advances in software support for high-throughput DNA sequencing: support for random, directed, and mixed sequencing strategies; a novel system for fragment assembly; a commercial object data-base management system for data storage; a client/server architecture for using network computational servers; and an underlying data model that can evolve to support fully automatic sequence reconstruction. GRM is currently being deployed for production use in high-throughput DNA sequencing projects.

Algorithms↗

PubMed1996

GenomeInspector: basic software tools for analysis of spatial correlations between genomic structures within megabase sequences.

The speed of acquisition of genomic sequence data exceeds the evaluation of function of the sequences by a vast margin. Most software available for the prediction of individual features does not assess the correlation of different motifs (level 1 methods). Here, we present a second-level software package called GenomeInspector (GI) for further analysis of results obtained with level 1 methods. Our approach does not require any a priori knowledge about motif organization and was designed as a modular package with a graphical user interface. Three examples for GI application are presented.

Genome↗

PubMed1999

Integrated mapping package--a physical mapping software tool kit.

We have developed an integrated physical mapping computer software package (IMP), originally designed to support the physical mapping of human chromosome 13 and expanded to support several gene-identification projects based on the positional candidate approach. IMP displays map data in a form that provides useful guidelines to the end users. An integrated map with high resolution and confidence is constructed from different types of mapping data, including hybridization experiments, STS-based PCR assays, genetic linkage mapping, cDNA localization, and FISH data. The map is also designed to provide suggestions for specific experiments that are required to obtain maps with even higher resolution and confidence. To this end, the optimization employs multiple constraints that take into account already established STS "scaffold" maps. This software thus serves as an important general tool kit for physical mapping, sequencing, and gene-hunting projects.

Algorithms↗

PubMed2001

Exploratory visualization software for reporting environmental survey results.

Environmental surveys yield three principal products: maps, a set of data tables, and a textual report. The relationships between these three elements, however, are often cumbersome to present, making full use of all the information in an integrated and systematic sense difficult. The published paper report is only a partial solution. Modern developments in computing, particularly in cartography, GIS, and hypertext, mean that it is increasingly possible to conceive of an easier and more interactive approach to the presentation of such survey results. Here, we present such an approach which links map and tabular datasets arising from a vegetation survey, allowing users ready access to a complex dataset using dynamic mapping techniques. Multimedia datasets equipped with software like this provide an exciting means of quick and easy visual data exploration and comparison. These techniques are gaining popularity across the sciences as scientists and decision-makers are presented with increasing amounts of diverse digital data. We believe that the software environment actively encourages users to make complex interrogations of the survey information, providing a new vehicle for the reader of an environmental survey report.

Conservation of Natural Resources↗

PubMed1999

EMAN: semiautomated software for high-resolution single-particle reconstructions.

We present EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs. The goal of this project is to provide software capable of performing single-particle reconstructions beyond 10 A as such high-resolution data become available. A complete single-particle reconstruction algorithm is implemented. Options are available to generate an initial model for particles with no symmetry, a single axis of rotational symmetry, or icosahedral symmetry. Model refinement is an iterative process, which utilizes classification by model-based projection matching. CTF (contrast transfer function) parameters are determined using a new paradigm in which data from multiple micrographs are fit simultaneously. Amplitude and phase CTF correction is then performed automatically as part of the refinement loop. A graphical user interface is provided, so even those with little image processing experience will be able to begin performing reconstructions. Advanced users can directly use the lower level shell commands and even expand the package utilizing EMAN's extensive image-processing library. The package was written from scratch in C++ and is provided free of charge on our Web site. We present an overview of the package as well as several conformance tests with simulated data.

Algorithms↗

PubMed1998

A new highly specific method for predicting the carcinogenic potential of pharmaceuticals in rodents using enhanced MCASE QSAR-ES software.

This report describes in detail a new quantitative structure-activity relational expert system (QSAR-ES) method for predicting the carcinogenic potential of pharmaceuticals and other organic chemicals in rodents, and a beta-test evaluation of its performance. The method employs an optimized, computer-automated structure evaluation (MCASE) software program and new database modules which were developed under a Cooperative Research and Development Agreement (CRADA) between FDA and Multicase, Inc. The beta-test utilized 126 compounds with carcinogenicity studies not included in control database modules and three sets of modules, including: A07-9 (Multicase, Inc.), AF1-4 (FDA-OTR/Multicase, Inc.), and AF5-8 (FDA-OTR/proprietary). The investigation demonstrated that the standard MCASE(A07-9) system which had a small data-set (n = 319), detected few structure alerts (SA) for carcinogenicity (n = 17), and had poor coverage for beta-test compounds (51%). Conversely, the new, optimized FDA-OTR/MCASE(AF5-8) system had a large data-set (n = 934), detected many SA (n = 58) and had good coverage (94%). In addition, the study showed the standard MCASE(A07-9) software had poor predictive value for carcinogens and specificity for noncarcinogens (50 and 42%), detected many false positives (58%), and exhibited poor concordance (46%). Conversely, the new, FDA-OTR/MCASE(AF5-8) system demonstrated excellent predictive value for carcinogens and specificity for non-carcinogens (97%, 98%), detected only one false positive (2%), and exhibited good concordance (75%). The dramatic improvements in the performance of the MCASE were due to numerous modifications, including: (a) enhancement of the size of the control database modules, (b) optimization of MCASE SAR assay evaluation criteria, (c) incorporation of a carcinogenic potency scale for control compound activity and MCASE biophores, (d) construction of individual rodent gender- and species-specific modules, and (e) defining assay acceptance criteria for query and control database compounds.

Animals↗