MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs

Background  

Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing.     

BBGD: an online database for blueberry genomic data

Background  

Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG) was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry.     

WebArray: an online platform for microarray data analysis

Background  

Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments.     

TmaDB: a repository for tissue microarray data

Background  

Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations (at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data.     

SASBDB: Towards an automatically curated and validated repository for biological scattering data

Small‐angle scattering (SAS) of X‐rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small‐angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org . SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user‐relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.     

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository

MOTIVATION: The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational methods. Software packages in the statistical environment R provide powerful tools for conducting such analyses. RESULTS: We introduce Rintact, a Bioconductor package that allows users to transform PSI-MI XML2.5 interaction data files from IntAct into R graph objects. On these, they can use methods from R and Bioconductor for a variety of tasks: determining cohesive subgraphs, computing summary statistics, fitting mathematical models to the data or rendering graphical layouts. Rintact provides a programmatic interface to the IntAct repository and allows the use of the analytic methods provided by R and Bioconductor. AVAILABILITY: Rintact is freely available at http://bioconductor.org     

Enhancing repository fungal data for biogeographic analyses

Open-access occurrence data are useful for studying spatial patterns of fungi, but often have quality issues. These include errors in taxonomy and geo-coordinates, and incomplete coverage across areas and taxonomic groups. We identify 15 quality issues that can lead to incorrect biogeographic inference, and develop a reproducible pipeline that flags and removes problematic entries. This pipeline tests accuracy of geographic records and names. Then, if information on non-native status is unavailable or unreliable, it detects non-native species via a predictive model. Finally, it identifies spatial and environmental outliers and removes them when biologically improbable. We test the pipeline by cleaning data for Australian fungi, with 251,642 records retained after cleaning the initial 1,034,601 records. Exploratory analysis showed that the cleaned data is useful for analyses such as biogeographic regionalisation, but recording gaps and lack of saturation in collection effort also caution that more surveys are needed to improve collection completeness.     

ProtaBank: A repository for protein design and engineering data

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user‐friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org .     

PeanutMap: an online genome database for comparative molecular maps of peanut

Background  

Molecular maps have been developed for many species, and are of particular importance for varietal development and comparative genomics. However, despite the existence of multiple sets of linkage maps, databases of these data are lacking for many species, including peanut.     

The plant phenological online database (PPODB): an online database for long-term phenological data

We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de.     

VisANT: an online visualization and analysis tool for biological interaction data

Background  

New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems.     

Segregation of FRAXE in a large family: clinical, psychometric, cytogenetic, and molecular data.

During an ongoing study on X-linked mental retardation, we ascertained a large family in which mild mental retardation was cosegregating with a fragile site at Xq27-28. Clinical, psychometric, cytogenetic, and molecular studies were performed. Apart from mild mental retardation, affected males and females did not show a specific clinical phenotype. Psychometric assessment of four representative affected individuals revealed low academic achievements, with verbal and performance IQs of 61-75 and 70-82, respectively. Cytogenetically the fragile site was always present in affected males and was not always present in affected females. With FISH the fragile site was located within the FRAXE region. The expanded GCC repeat of FRAXE was seen in affected males and females either as a discrete band or as a broad smear. No expansion was seen in unaffected males, whereas three unaffected females did have an enlarged GCC repeat. Maternal transmission of FRAXE may lead to expansion or contraction of the GCC repeat length, whereas in all cases of paternal transmission contraction was seen. In striking contrast to the situation in fragile X syndrome, affected males may have affected daughters. In addition, there appears to be no premutation of the FRAXE GCC repeat, since in the family studied here all males lacking the normal allele were found to be affected.     

Microarray gene expression database: progress towards an international repository of gene expression data

A report on the third Microarray Gene Expression Database group meeting (MGED3), Stanford University, Palo Alto, California, USA, 29-31 March, 2001.     

CyDAS: a cytogenetic data analysis system

For statistical analyses in cancer cytogenetics, the genomic changes encoded by the karyotype must be translated into numerical codes. We developed a program, which extracts chromosomal gains and losses as well as breakpoints from the karyotype. The changes are compiled in tables according to the chromosome bands involved and/or depicted in projection to the respective chromosome ideogram. The data are ready to be integrated into further statistical analyses. The program may be run as desktop or Internet application.     

Enhancing data mobilisation through a centralised data repository for Atlantic salmon (Salmo salar L.): Providing the resources to promote an ecosystem-based management framework.

Data and knowledge mobilisation are significant challenges in ecology and resource management, with the journey from data collection through to management action often left incomplete due to difficulties sharing information across diverse and dispersed communities. This disconnect between science and management must be resolved if we are to successfully tackle the increasing impact of human activity on our ecosystems. Across their North Atlantic range, Atlantic salmon (Salmo salar L.) populations are in steep decline in many areas and urgent actions are required to curb this decline. Being commercially important this species has been subject to intense research, but management action often suffers from both a lack of access to this knowledge resource and support for its integration into effective management strategies. To respond to this challenge, the science and management communities must place higher priority on mobilising existing and emerging knowledge sources to inform current and future resource use and mitigation strategies. This approach requires a more complete picture of the current salmon ecology data and knowledge landscape, new mechanisms to enable data mobilisation and re-use, and new research to describe and parameterise the responses of wild populations to habitat changes. Here we present a unique interface for registering and linking data resources relevant to the Atlantic salmon life cycle that can address the data mobilisation aspect of these challenges. The Salmon Ecosystem Data Hub is a salmon-specific metadata catalogue, natively interoperable with many existing data portals, which creates a low resistance pathway to maximise visibility of data relevant to Atlantic salmon. This includes the capacity to annotate datasets with life-stage domains and variable classes, thereby permitting dispersed data to be formally contextualised and integrated to support hypotheses specific to scenario-based modelling and decision-making. The alignment and mobilisation of data within the Salmon Ecosystem Data Hub will help advance the development of appropriate environmentally driven forecast models and an ecosystem-based management approach for Atlantic salmon that optimises future management strategies.     

Cryptic Caribbean species of Scorpaena (Actinopterygii: Scorpaeniformes) suggested by cytogenetic and molecular data

Cytogenetic and molecular analyses enabled identification of two cytotypes among individuals of the spotted scorpion fish Scorpaena plumieri from Margarita Island, Venezuela. Cytotype 1 was characterized by 48 subtelo‐acrocentric chromosomes and fundamental number (number of chromosome arms; FN) equalled 48, while cytotype 2 was characterized by two metacentric and 46 subtelo‐acrocentric chromosomes and FN was 50. These cytotypes also differed in the location of the ribosomal gene clusters and in the distribution of the constitutive heterochromatin. Moreover, fish from the cytotypes 1 and 2 were found to belong to distinct mitochondrial lineages. The presence of two S. plumieri cytotypes from two lineages separated by high genetic distance suggests that they correspond to sympatric cryptic species.     

High molecular weight DNA from fixed cytogenetic preparations.

Cell pellets that have been stored in routine clinical cytogenetic fixative were studied for the presence of intact DNA. A method for the isolation of high molecular weight DNA from fixed cytogenetic preparations of human leukocytes, bone marrow, and cell hybrid cultures is presented. DNA preparations from fixed pellets were cleaved with restriction enzymes, transferred to nitrocellulose filters after agarose gel electrophoresis, and hybridized to radiolabeled probes to demonstrate that fixed cell pellets could yield DNA of sufficient quality for Southern blot hybridization analysis. This protocol may be useful for molecular analysis of DNA from fixed cell pellets of patients who are unavailable for additional sampling.     

MicroMeasure: a new computer program for the collection and analysis of cytogenetic data.

The ability to identify individual chromosomes in cytological preparations is an essential component of many investigations. While several computer software applications have been used to facilitate such quantitative karyotype analysis, most of these programs are limited by design for specific types of analyses, or can be used only with specific hardware configurations. MicroMeasure is a new image analysis application that may be used to collect data for a wide variety of chromosomal parameters from electronically captured or scanned images. Unlike similar applications, MicroMeasure may be individually configured by the end user to suit a wide variety of research needs. This program can be used with most common personal computers, and requires no unusual or specific hardware. MicroMeasure is made available to the research community without cost by the Department of Biology at Colorado State University via the World Wide Web at http://www.biology.colostate.edu/MicroMeasure.