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.     

Habitat suitability for wisents in the Carpathians – a model based on presence only data

The study tested an alternative method for the evaluation of habitat preferences of wisents (Bison bonasus) based upon possibly non-biased dataset – presence only data. Data on spatial distribution of free-ranging wisents (3055 individual presence records) were collected over a period of 10 years in the Bieszczady Mountains, south-eastern Poland. Using a nonparametric method of kernel estimators, the density of animal occurrence was calculated. The obtained dot map distribution allowed for spatial analyses of seasonal (winter and vegetative) presence that is related to environmental parameters such as the type of forest stand, dominating tree species, terrain and aspect. According to the final log-linear model, based upon presence-only data, significant differences exist in wisent seasonal preferences for habitat type. Wisents were more commonly found, in both winter and vegetative seasons, on sites with broken canopy closure (85.71% and 86.44%, respectively), as well as on slopes with steepness of 13-17^o, with rate of presence of 89.83% and 91.84%, respectively. The most frequented tree association was alnus/pine irrespective of season. During both seasons, the percentage of records of wisent presence was the highest within sites of north aspect (93.22% in winter and 93.88% in vegetative), and on sloping terrain (94.92% and 93.88%, respectively), rather than within valleys or areas of relative flatness. The obtained results allow identification of conditions optimal for those animals unbiased by subjective evaluation of habitat conditions. This approach can be crucial in selecting sites potentially suitable for future reintroductions of wisents in the whole Carpathian range.     

The IAEA Radiotracer Biodistribution Template – A community resource for supporting the standardization and reporting of radionuclide pre-dosimetry data

Radionuclide absorbed-dose dosimetry is an active area of development and has the potential to positively impact molecular radiotherapies. At present, many of the operations required to perform dosimetry calculations are unstandardized and unestablished. While the current methodology allows reasonable dosimetry estimates to be derived and published, it can be difficult to understand, and reproduce, each others’ work. To help alleviate this we have identified the collection of biodistribution information as a key step in all internal dosimetry calculations, and present a template that can be used to standardize its documentation and reporting.A generalized biodistribution template entitled the IAEA Radiotracer Biodistribution Template (IAEA RaBiT) has been built and distributed for users performing biodistribution measurements in the community. The template enables robust recording of dosimetry-relevant information through standardization of details and their format. It has been designed to be simple and easy to use, and establish a structured recording of a common reference point in dosimetry operations – biodistribution data documentation. Improved documentation procedures may benefit organization of in house data, or be used to disseminate details throughout the community – for example to supplement dosimetry related publications. The standard format information may also enable the creation of new dosimetry related tools and protocols and support robust population databases.As dosimetry in nuclear medicine becomes more routinely applied in clinical applications, we need to develop the infrastructure for robustly handling large amounts of these data. Our IAEA RaBiT can be used as a standard format structure for data collection, organization, and dissemination.     

LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

Background  

Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, highly complex and noisy. Accordingly, it has sparked new developments in Bioinformatics, especially in the fields of algorithm development, statistics and software engineering. In a quantitative label-free mass spectrometry experiment, crucial steps are the detection of peptide features in the mass spectra and the alignment of samples by correcting for shifts in retention time. At the moment, it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists only for peptide identification algorithms but no data that represents a ground truth for the evaluation of feature detection, alignment and filtering algorithms.     

2DDB – a bioinformatics solution for analysis of quantitative proteomics data

Background  

We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.     

NeuroTerrain – a client-server system for browsing 3D biomedical image data sets

Background  

Three dimensional biomedical image sets are becoming ubiquitous, along with the canonical atlases providing the necessary spatial context for analysis. To make full use of these 3D image sets, one must be able to present views for 2D display, either surface renderings or 2D cross-sections through the data. Typical display software is limited to presentations along one of the three orthogonal anatomical axes (coronal, horizontal, or sagittal). However, data sets precisely oriented along the major axes are rare. To make fullest use of these datasets, one must reasonably match the atlas' orientation; this involves resampling the atlas in planes matched to the data set. Traditionally, this requires the atlas and browser reside on the user's desktop; unfortunately, in addition to being monolithic programs, these tools often require substantial local resources. In this article, we describe a network-capable, client-server framework to slice and visualize 3D atlases at off-axis angles, along with an open client architecture and development kit to support integration into complex data analysis environments.     

stam – a Bioconductor compliant R package for structured analysis of microarray data

Background  

Genome wide microarray studies have the potential to unveil novel disease entities. Clinically homogeneous groups of patients can have diverse gene expression profiles. The definition of novel subclasses based on gene expression is a difficult problem not addressed systematically by currently available software tools.     

CMA – a comprehensive Bioconductor package for supervised classification with high dimensional data

Background  

For the last eight years, microarray-based classification has been a major topic in statistics, bioinformatics and biomedicine research. Traditional methods often yield unsatisfactory results or may even be inapplicable in the so-called "p ≫ n" setting where the number of predictors p by far exceeds the number of observations n, hence the term "ill-posed-problem". Careful model selection and evaluation satisfying accepted good-practice standards is a very complex task for statisticians without experience in this area or for scientists with limited statistical background. The multiplicity of available methods for class prediction based on high-dimensional data is an additional practical challenge for inexperienced researchers.     

Data – ova – gene – data

In this essay, I observe that data is valuable not only for what it is, but also for what it will become: that is, that data is a form of potential. I explore two aspects of this by drawing two comparisons with other forms of potential: ova and genes. First, building on ethnographic fieldwork with environmental scientists and technicians in the Brazilian Amazon, I compare data processing with ova donation in the United Kingdom in order to explore how data processing might be considered a form of reproductive labour. I then turn to emergent big data infrastructures in the environmental sciences, and compare the environmental sciences with genomics, in order to gesture towards some critical questions that need to be asked of such open data initiatives. I end with a reflection on comparison as a privileged means of drawing out the forms understood to be latent within data.     

TableButler – a Windows based tool for processing large data tables generated with high-throughput methods

Background  

High-throughput "omics" based data analysis play emerging roles in life sciences and molecular diagnostics. This emphasizes the urgent need for user-friendly windows-based software interfaces that could process the diversity of large tab-delimited raw data files generated by these methods. Depending on the study, dozens to hundreds of these data tables are generated. Before the actual statistical or cluster analysis, these data tables have to be combined and merged to expression matrices (e.g., in case of gene expression analysis). Gene annotations as well as information concerning the samples analyzed may be appended, renewed or extended. Often additional data values shall be computed or certain features must be filtered out.     

qTROSY – a novel scheme for recovery of the anti-TROSY magnetisation

In TROSY experiments, spin state selection (S³) retains only the single HSQC sub-spectrum with minimal T₂ relaxation and maximal resolution, yet at the cost of eliminating half of the available polarisation as undesired anti-TROSY component. We here introduce queued TROSY (qTROSY) as a novel scheme to partially recover and exploit this anti-TROSY polarisation in two concatenated scans. After initial orthogonal spin state separation (oS³), anti-TROSY polarisation is explicitly stored while its TROSY counterpart follows the desired coherence pathway recorded in a first scan A. The immediately appended scan B then quantitatively converts the recovered anti-TROSY polarisation into a second TROSY spectrum, skipping the time-limiting long reequilibration delay. Both concatenated qTROSY scans thus ideally exploit the full initial polarisation within almost the same measurement time. In practice, T₂ relaxation losses accruing during the coupling evolution delays reduced anti-TROSY polarisation recovery below 40%, obviating sensitivity enhancement through addition of both qTROSY scans; yet, scan B retained a complete scan A spectrum with up to 75% intensity. We therefore propose to employ qTROSY asymmetrically, compacting two separate conventional into one queued TROSY-type experiment with significantly reduced measurement time, implying primarily the concatenation of different three- or higher-dimensional experiments. Both anti-TROSY polarisation recoveries and possible time savings are largest for deuterated and smaller non-deuterated proteins, extending the rentability limit of the TROSY principle towards smaller molecular weights.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-5618-z     

tacg – a grep for DNA

Background  

Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple motifs with IUPAC degeneracies, regular expressions, patterns allowing mismatches, and probability matrices.     

SNA – a toolbox for the stoichiometric analysis of metabolic networks

Background  

Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem.     

The glomerulus – a view from the outside – the podocyte

In the past decade, podocyte research has been greatly aided by the development of powerful new molecular, cellular and animal tools, leading to elucidation of an increasing number of proteins involved in podocyte function and identification of mutated genes in hereditary glomerulopathies. Accumulating evidence indicates that podocyte disorders may not only underlie these hereditary glomerulopathies but also play crucial role in a broad spectrum of acquired glomerular diseases. Genetic susceptibility, environmental influence and systemic responses are all involved in the mediation of the pathogenesis of podocytopathies. Injured podocytes may predisopose to further injury of other podocytes and other adjacent/distant renal cells in a vicious cycle, leading to inexorable progression of glomerular injury. The classic view is that podocytes have a limited ability to proliferate in the normal mature kidney. However, recent research in rodents has provided suggestive evidence for podocyte regeneration resulting from differentiation of progenitor cells within Bowman's capsule.     

CGHPRO – A comprehensive data analysis tool for array CGH

Background  

Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios.     

DEEMY – the concept of a characterization and determination system for ectomycorrhizae

 A considerable amount of data has been published on morphological and anatomical characteristics of ectomycorrhizae but these are dispersed in several, sometimes not easily available, journals. The few keys that exist are mostly based upon host tree genera. No comprehensive determination tools for non-experts are available. An information system for specific characters of ectomycorrhizae and an interactive key are now provided by DEEMY on CD-ROM. Accepted: 6 May 1997