Computers: the best friends a human genome ever had

Mapping and sequencing the human genome will generate large amounts of data, which must be sorted, analyzed, and stored for rapid retrieval to complete this enormous task. Computers and their software programs provide the most important tool to the molecular biologist today. A discussion of current capabilities and future needs in computer hardware and software for the human genome project is the topic of this paper. The use of computer programs to generate restriction maps, manage clone libraries, manage sequence projects, and generate consensus sequences is presented. The use of computers to communicate useful information rapidly to scientific colleagues is also mentioned. The role of both GenBank and BIONET is central to the dissemination and analysis of sequence information. The capabilities of electronic communication worldwide for assisting this project is available on the BIONET National Computer Resource, using existing networks.     

New developments at BIONET

BIONET has made considerable progress in developing communication links among molecular biologists and biochemists worldwide. We describe these efforts and also note the many new enhancements to the BIONET system itself.     

Protein kinase resource: an integrated environment for phosphorylation research

The protein kinase superfamily is an important group of enzymes controlling cellular signaling cascades. The increasing amount of available experimental data provides a foundation for deeper understanding of details of signaling systems and the underlying cellular processes. Here, we describe the Protein Kinase Resource, an integrated online service that provides access to information relevant to cell signaling and enables kinase researchers to visualize and analyze the data directly in an online environment. The data set is synchronized with Uniprot and Protein Data Bank (PDB) databases and is regularly updated and verified. Additional annotation includes interactive display of domain composition, cross-references between orthologs and functional mapping to OMIM records. The Protein Kinase Resource provides an integrated view of the protein kinase superfamily by linking data with their visual representation. Thus, human kinases can be mapped onto the human kinome tree via an interactive display. Sequence and structure data can be easily displayed using applications developed for the PKR and integrated with the website and the underlying database. Advanced search mechanisms, such as multiparameter lookup, sequence pattern, and blast search, enable fast access to the desired information, while statistics tools provide the ability to analyze the relationships among the kinases under study. The integration of data presentation and visualization implemented in the Protein Kinase Resource can be adapted by other online providers of scientific data and should become an effective way to access available experimental information.     

Optimal alignments in linear space

Space, not time, is often the limiting factor when computingoptimal sequence alignments, and a number of recent papers inthe biology literature have proposed space-saving strategies.However, a 1975 computer science paper by Hirschberg presenteda method that is superior to the new proposals, both in theoryand in practice. The goal of this paper is to give Hirschberg'sidea the visibility it deserves by developing a linear-spaceversion of Gotoh's algorithm, which accommodates affine gappenalties. A portable C-software package implementing this algorithmis available on the BIONET free of charge. Received on October 14, 1987; accepted on December 19, 1987     

An authorization framework for metacomputing applications

To span administrative boundaries, metacomputing systems require the integration of strong authentication and authorization methods. The problem is complicated because different components of the system may have different security policies. This paper presents a distributed model for authorization that we have integrated with the Prospero Resource Manager, a metacomputing resource allocation system developed at USC. The integration of authorization with PRM was accomplished through the specification of a policy language and the use of a Generic Authorization and Access-control API (GAA API). The language supports the specification of diverse authorization policies including ACLs, capabilities and lattice-based access controls. The GAA API provides a uniform authorization service interface for facilitating access control decisions and requesting authorization information about a particular resource. We describe a prototype of our system. This revised version was published online in July 2006 with corrections to the Cover Date.     

The protein identification resource (PIR)

The Protein Identification Resource consists of an integrated computer system composed of a number of protein and nucleic acid sequence databases and software designed for the identification and analysis of protein sequences and their corresponding coding sequences. The PIR serves the scientific community through on-line access, distributing magnetic tapes, and performing off-line sequence identification services for researchers.     

Social rank and habitat use in willow tit groups

One view depiets dominance and subordination as roles with equal fitness played as parts of a mixed behavioural strategy, but subordination can also be maintained as a transient strategy of ‘hopeful dominants’. Resource access in groups of non-kin willow tits, Parus montanus, was related to social rank. Dominants excluded subordinates from the preferred microhabitat. Fitness in terms of survival was correlated with access to the preferred foraging sites, indicating that a mixed-strategy explanation is inadequate. Social rank was linked to age, and first-year subordinates behaved as predicted for hopeful dominants. They were not ‘herded’ by dominant group mates because subordinates actively maintained contact with dominants. One possible reason for subordinates joining winter groups might be the opportunity to reduce dominants' pay-off from aggression.     

The effects of female control of resources on sex-differentiated mate preferences

A number of sex differences in mate preferences have been reported across cultures. Women prefer partners who are older than them whereas men prefer partners who are younger than them. Women have stronger preferences for resource-acquisition characteristics whereas men have stronger preferences for physical attractiveness. Recently, studies have reported shifts in female preferences with increasing female empowerment and associated female attitudes. Other studies, however, report opposite effects of female wealth and income. In this study, we investigated the effects of female control of the resources necessary to raise offspring successfully on mate preferences. We developed measures of resource control at the level of the individual and investigated relationships between these and mate preferences using an internet survey. Resource control was associated with preferences for physical attractiveness over good financial prospects and greater maximum partner age tolerated. Resource control, however, was also associated with tolerance of younger partners. The results implicate the role of constraints on female access to and control of resources in sex-differentiated mate preferences and highlight differences between resource control and wealth.     

Food distribution,dominance, and aggressive behaviors in bonnet macaques

Resource availability or distribution may affect interindividual competition in species such as primates, which forage in social groups, and several field studies suggest that dominance status predicts access to restricted food sources. Increased competition due to restricted resources may result in the intensification of aggressive behaviors. The study reported here examines the impact of manipulation of the distribution of food resources in a laboratory-housed group of bonnet macaques to assess the impact of distribution on aggressive behaviors. Food was restricted to a space which allowed access to only one or two individuals at a time or was dispersed throughout the living enclosure to allow universal access in alternating periods. During periods of clumped distribution, the monkeys obtained access to the food in order of their dominance status in the group. In addition, overall levels of aggressive behaviors increased, submissive behavior increased, and play decreased during periods of clumped distribution of food. These results confirm the findings from field studies indicating increases in agonism with restriction of food resources. These findings also have implications for primate colony management, in terms of developing strategies for minimizing intragroup aggression in captive groups.     

Operational Changes in a Shared Resource Laboratory with the Use of a Product Lifecycle Management Approach: A Case Study

Shared Resource Laboratories (SRLs) provide investigators access to necessary scientific and resource expertise to leverage complex technologies fully for advancing high-quality biomedical research in a cost-effective manner. At the University of Nebraska Medical Center, the Flow Cytometry Research Facility (FCRF) offered access to exceptional technology, but the methods of operation were outdated and unsustainable. Whereas technology has advanced and the institute has expanded, the operations at the facility remained unchanged for 35 yr. To rectify this, at the end of 2013, we took a product lifecycle management approach to affect large operational changes and align the services offered with the SRL goal of education, as well as to provide service to researchers. These disruptive operational changes took over 10 mo to complete and allowed for independent end-user acquisition of flow cytometry data. The results have been monitored for the past 12 mo. The operational changes have had a positive impact on the quality of research, increased investigator-facility interaction, reduced stress of facility staff, and increased overall use of the resources. This product lifecycle management approach to facility operations allowed us to conceive of, design, implement, and monitor effectively the changes at the FCRF. This approach should be considered by SRL management when faced with the need for operationally disruptive measures.     

MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms

MonkeySNP is a web-based resource created by the Genetic Resource and Informatics Program at the Oregon National Primate Research Center to facilitate access to non-human primate (NHP) single nucleotide polymorphisms (SNP) data. MonkeySNP is a mirror of the NCBI dbSNP database and contains additional NHP subpopulation genotype data and visual genotype displays to support SNP review and selection. AVAILABILITY: http://monkeysnp.ohsu.edu/snp/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).     

AraCyc: a biochemical pathway database for Arabidopsis

AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).     

ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis

Protein interactions are fundamental to the molecular processes occurring within an organism and can be utilized in network biology to help organize, simplify, and understand biological complexity. Currently, there are more than 10 publicly available Arabidopsis (Arabidopsis thaliana) protein interaction databases. However, there are limitations with these databases, including different types of interaction evidence, a lack of defined standards for protein identifiers, differing levels of information, and, critically, a lack of integration between them. In this paper, we present an interactive bioinformatics Web tool, ANAP (Arabidopsis Network Analysis Pipeline), which serves to effectively integrate the different data sets and maximize access to available data. ANAP has been developed for Arabidopsis protein interaction integration and network-based study to facilitate functional protein network analysis. ANAP integrates 11 Arabidopsis protein interaction databases, comprising 201,699 unique protein interaction pairs, 15,208 identifiers (including 11,931 The Arabidopsis Information Resource Arabidopsis Genome Initiative codes), 89 interaction detection methods, 73 species that interact with Arabidopsis, and 6,161 references. ANAP can be used as a knowledge base for constructing protein interaction networks based on user input and supports both direct and indirect interaction analysis. It has an intuitive graphical interface allowing easy network visualization and provides extensive detailed evidence for each interaction. In addition, ANAP displays the gene and protein annotation in the generated interactive network with links to The Arabidopsis Information Resource, the AtGenExpress Visualization Tool, the Arabidopsis 1,001 Genomes GBrowse, the Protein Knowledgebase, the Kyoto Encyclopedia of Genes and Genomes, and the Ensembl Genome Browser to significantly aid functional network analysis. The tool is available open access at http://gmdd.shgmo.org/Computational-Biology/ANAP.     

An intellectual property sharing initiative in agricultural biotechnology: development of broadly accessible technologies for plant transformation

The Public Intellectual Property Resource for Agriculture (PIPRA) was founded in 2004 by the Rockefeller Foundation in response to concerns that public investments in agricultural biotechnology benefiting developing countries were facing delays, high transaction costs and lack of access to important technologies due to intellectual property right (IPR) issues. From its inception, PIPRA has worked broadly to support a wide range of research in the public sector, in specialty and minor acreage crops as well as crops important to food security in developing countries. In this paper, we review PIPRA's work, discussing the failures, successes, and lessons learned during its years of operation. To address public sector's limited freedom-to-operate, or legal access to third-party rights, in the area of plant transformation, we describe PIPRA's patent 'pool' approach to develop open-access technologies for plant transformation which consolidate patent and tangible property rights in marker-free vector systems. The plant transformation system has been licensed and deployed for both commercial and humanitarian applications in the United States (US) and Africa, respectively.     

JDotter: a Java interface to multiple dotplots generated by dotter

Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. AVAILABILITY: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. SUPPLEMENTARY INFORMATION: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.     

The Nuclear Receptor Resource Project.

We have expanded the original Glucocorticoid Receptor Resource (GRR) database to include several individual resources as part of a larger project called the Nuclear Receptor Resource (NRR). In addition to the GRR, the NRR currently features the Thyroid Hormone Receptor Resource, the Androgen Receptor Resource, the Mineralocorticoid Receptor Resource, the Vitamin D Receptor Resource, and the Steroid Receptor Associated Proteins Resource. The goal of the NRR project is to provide a comprehensive resource for information on the nuclear receptor superfamily, and to provide a forum for the dissemination and discussion of both published and unpublished material on these proteins. Although the individual resources are managed from different servers, all the files are integrated and can be accessed through the project's Home Page, housed at http://nrr. georgetown.edu/nrr.html. In the near future, we hope to expand the project to contain information on other nuclear receptors and to better our electronic publication system. To accomplish this, we encourage the involvement of nuclear receptor investigators in the NRR.     

Resource characteristics and competition affect colony and individual foraging strategies of the wood ant Formica integroides

Abstract.  1. Resource characteristics and competitive pressure can affect an ant colony's foraging strategy. This study examined the ability of the wood ant Formica integroides to respond, at both the colony and individual levels, to changes in competitive pressure for access to terrestrial and arboreal resources.
2. Because foraging behaviours depend on resource characteristics, foraging for different resource types (e.g. terrestrial and arboreal habitats) produces different spatial or territorial arrangements. In this study, terrestrial contests for resources followed an interference-exploitation tradeoff, while arboreal foragers defended entire trees as absolute territories.
3. Competitive pressure for access to arboreal resources was shown to increase with distance from F. integroides nests.
4. In this study, the ability of F. integroides to defend a resource varied with body size. Large foragers were better defenders than small foragers. For groups of foragers, the ability to defend a resource increased with the ratio of large to small foragers.
5. In response to competitive pressure, F. integroides colonies altered the size distribution of arboreal, but not terrestrial, foragers. An increase in competitive pressure was matched by an increase in the number of large foragers allocated to trees. This response to competition affected the relationship between body size and distance from the nest for arboreal foragers.
6. Foraging behaviours for individual arboreal foragers also varied with competitive pressure. As competition increased, large arboreal foragers spent more time in direct contact with the resource rather than standing between resource patches.     

Making access to health care more equal: the role of general medical services.

The Resource Allocation Working Party (RAWP) recognised the need to consider both health authority and primary care services in achieving its objective. RAWP and the subsequent Advisory Group on Resource Allocation (AGRA) found (but did not publish) considerable variation in resources used by both services but could not find a clear relation between them. Statistics provided by the DHSS were used to compare spending by 80 area health authorities in 1980-1 with expenditure per head on general medical services by their corresponding family practitioner committees. There was considerable variation in the provision of resources for both services and no clear relation between the variations in spending on each service. Only 40 of the 80 areas had both health authority and family practitioner committee spending levels within 10% of "target." Subregional inequalities in resources tend to be related to variations in admission rates, which in turn are related to general practitioners'' referral behaviour. These results emphasise the importance of finding out more about inequalities in the provision of general medical services and their relation to the use of hospital services. They also suggest that RAWP''s aim of equality of opportunity of access to health care resources may be achieved only if general medical services are brought into the equation as well.