Natural hybridization in heliconiine butterflies: the species boundary as a continuum

Background  

To understand speciation and the maintenance of taxa as separate entities, we need information about natural hybridization and gene flow among species.     

GeneLibrarian: an effective gene-information summarization and visualization system

Background  

Abundant information about gene products is stored in online searchable databases such as annotation or literature. To efficiently obtain and digest such information, there is a pressing need for automated information-summarization and functional-similarity clustering of genes.     

PEPOP: Computational design of immunogenic peptides

Background  

Most methods available to predict protein epitopes are sequence based. There is a need for methods using 3D information for prediction of discontinuous epitopes and derived immunogenic peptides.     

Consistency,comprehensiveness, and compatibility of pathway databases

Background  

It is necessary to analyze microarray experiments together with biological information to make better biological inferences. We investigate the adequacy of current biological databases to address this need.     

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

Background  

Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.     

GOLD.db: genomics of lipid-associated disorders database

Background  

The GOLD.db (Genomics of Lipid-Associated Disorders Database) was developed to address the need for integrating disparate information on the function and properties of genes and their products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders.     

Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation

Background  

With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent results of the exploratory analysis on the web in an easy-to-comprehend form and to facilitate convenient information retrieval.     

Identification of consensus RNA secondary structures using suffix arrays

Background  

The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. However, an alignment is often difficult to obtain without prior structural information. Thus the need for tools to automate this process.     

A case study in pathway knowledgebase verification

Background  

Biological databases and pathway knowledgebases are proliferating rapidly. We are developing software tools for computer-aided hypothesis design and evaluation, and we would like our tools to take advantage of the information stored in these repositories. But before we can reliably use a pathway knowledgebase as a data source, we need to proofread it to ensure that it can fully support computer-aided information integration and inference.     

SIDEKICK: Genomic data driven analysis and decision-making framework

Background  

Scientists striving to unlock mysteries within complex biological systems face myriad barriers in effectively integrating available information to enhance their understanding. While experimental techniques and available data sources are rapidly evolving, useful information is dispersed across a variety of sources, and sources of the same information often do not use the same format or nomenclature. To harness these expanding resources, scientists need tools that bridge nomenclature differences and allow them to integrate, organize, and evaluate the quality of information without extensive computation.     

MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences

Background  

The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.     

Tool for the environmental assessment of cranes based on parameterization

Purpose  

Information constitutes one of the main barriers for applying life cycle assessment (LCA) due to complexity and need for great amounts of it. However, most of the parameters that determine the data are defined early in the product development process. Knuckle boom cranes constitute a complex product which poses a particularly pressing need for simplification. This paper models the LCA inventory information out of design parameters. The paper also presents a tool implementing this.     

Isolation, identification and expression analysis of salt-induced genes in Suaeda maritima, a natural halophyte, using PCR-based suppression subtractive hybridization

Background  

Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. Thus, there is a need of continued effort to understand the salt tolerance mechanism using suitable biotechnological techniques and test plants (species) to enable development of salt tolerant cultivars of interest. Therefore, the present study was undertaken to generate information on salt stress responsive genes in a natural halophyte, Suaeda maritima, using PCR-based suppression subtractive hybridization (PCR-SSH) technique.     

BACTIBASE: a new web-accessible database for bacteriocin characterization

Background  

Bacteriocins are very diverse group of antimicrobial peptides produced by a wide range of bacteria and known for their inhibitory activity against various human and animal pathogens. Although many bacteriocins are now well characterized, much information is still missing or is unavailable to potential users. The assembly of such information in one central resource such as a database would therefore be of great benefit to the exploitation of these bioactive molecules in the present context of increasing antibiotic resistance and natural bio-preservation need.     

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

Background  

New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.     

Skittle: A 2-Dimensional Genome Visualization Tool

Background  

It is increasingly evident that there are multiple and overlapping patterns within the genome, and that these patterns contain different types of information - regarding both genome function and genome history. In order to discover additional genomic patterns which may have biological significance, novel strategies are required. To partially address this need, we introduce a new data visualization tool entitled Skittle.     

Biana: a software framework for compiling biological interactions and analyzing networks

Background  

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.     

Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains

Background  

The subcellular location of a protein is closely related to its function. It would be worthwhile to develop a method to predict the subcellular location for a given protein when only the amino acid sequence of the protein is known. Although many efforts have been made to predict subcellular location from sequence information only, there is the need for further research to improve the accuracy of prediction.     

MolTalk – a programming library for protein structures and structure analysis

Background  

Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn.     

Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions

Background  

The amount of data on protein-protein interactions (PPIs) available in public databases and in the literature has rapidly expanded in recent years. PPI data can provide useful information for researchers in pharmacology and medicine as well as those in interactome studies. There is urgent need for a novel methodology or software allowing the efficient utilization of PPI data in pharmacology and medicine.