IdBean: a Java GUI application for conversion of biological identifiers

We have developed a biologist-friendly, stand-alone Java GUI application, IdBean, for ID conversion. Our tool integrated most of the widely used ID conversion services that provide programmatic access. It is the first GUI ID conversion application that supports the direct merging as well as comparison of conversion results from multiple ID conversion services without manual effort. This tool will greatly help biologists who handle multiple ID types for the analyses of gene or gene product lists. By referring to multiple conversion services, the number of failed IDs can be reduced. By accessing ID conversion service online, it will potentially provide the most up-to-date conversion results. The application was developed in modular form; however, it can be re-packaged into plug-in form. For the development of a bioinformatics analysis tool, the module can be used as a built-in ID conversion component. It is available at http://neon.gachon.ac.kr/IdBean/.     

GoBean: a Java GUI application for visual exploration of GO term enrichments

We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of analysis results. The program includes many essential and useful features, such as enrichment analysis algorithms, multiple test correction methods, and versatile filtering of enriched GO terms for more focused analyses. A unique graphic interface reflecting the GO tree structure was devised to facilitate comparisons of multiple GO analysis results, which can provide valuable insights for biological interpretation. Additional features to enhance user convenience include built in ID conversion, evidence code-based gene-GO association filtering, set operations of gene lists and enriched GO terms, and user -provided data files. It is available at http://neon.gachon.ac.kr/GoBean/.     

Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

Background  

Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context.     

Sugar-cane breeding in Java

Hybridization work and commercial introduction of many new clones into the sugar plantations of this island have resulted in a tenfold increase in sugar production on an acreage basis since 1840.     

Colonial Capitalism in Java

Control of Land and Labour in Colonial Java. By Jan Breman Javanese Peasants and the Colonial Sugar Industry. By R.E. Elson     

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background  

Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures.     

Experience in application of databases of bloodsucking insects to zoological studies

The paper summarizes our long-term experience of accumulating and summarizing the faunistic information by means of separate databases (DB) and information-analytic systems (IAS), and also prospects of its representation by modern multi-user information systems. The experience obtained during development and use of the IAS PARHOST1 for the study of the world flea fauna and work with partial databases created for the study of bloodsucking insects (lice and blackflies) is analyzed. Research collection material of the type series of 57 species and subspecies of fleas of the fauna of Russia was made available via a multi-user information retrieval system on the Internet portal of the Zoological Institute of the Russian Academy of Sciences. The system provides the means of storing information in its authentic form as well as its gradual transformation, i.e., unification and structuring. In order to ensure ceaseless DB update, the possibility of work of operators with different levels of competence is provided.     

CLANS: a Java application for visualizing protein families based on pairwise similarity

SUMMARY: The main source of hypotheses on the structure and function of new proteins is their homology to proteins with known properties. Homologous relationships are typically established through sequence similarity searches, multiple alignments and phylogenetic reconstruction. In cases where the number of potential relationships is large, for example in P-loop NTPases with many thousands of members, alignments and phylogenies become computationally demanding, accumulate errors and lose resolution. In search of a better way to analyze relationships in large sequence datasets we have developed a Java application, CLANS (CLuster ANalysis of Sequences), which uses a version of the Fruchterman-Reingold graph layout algorithm to visualize pairwise sequence similarities in either two-dimensional or three-dimensional space. AVAILABILITY: CLANS can be downloaded at http://protevo.eb.tuebingen.mpg.de/download.     

Canada produces its first MD specializing in telemedicine

Originally Dr. Rod Elford had planned to pursue a career in sports medicine. An introduction to space medicine and the possibilities inherent in telemedicine changed all that, and last year he became the first Canadian physician to complete a clinical fellowship in this emerging field. Observers think he is likely to be the first of many.     

Syncretism and the Politics of the Tingkeban in West Java

For the rural Sundanese of West Java who identify with Nahdatul Ulama Islam, the tingkeban is considered a mandatory ritual to be conducted for a woman who is seven months pregnant. However, like other local practices around birth, the tingkeban has come under state and urban modernising influences that have attempted to displace some of its elements as ‘culture’ rather than ‘religion’ and to discredit many of these as superstitious and backward. This paper examines the ritual elements of the tingkeban that produce and reinforce local cosmological and ontological ideas about the nature of personhood and society, and, in particular, how the ritual highlights the ambivalent status of the villagers within broader relations of power such as the Indonesian State and other forms of Islam existing in Indonesia. The paper also explores how the assumptions within the ideology of modernisation propagated under the last years of the Suharto regime coincide with assumptions in scholarly work such as those underlying Geertz's depiction of the syncretic nature of Javanese religion.     

JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation

SUMMARY: The characterization of deleterious genomic mutation (DGM) is of central significance for evolutionary biology and genetic studies. Fitness moment method has been developed to efficiently characterize DGM from natural population directly. In order to enable researchers to employ this method for theoretical and empirical research on characterizing DGM, we here present a distributed Java Application for DGM Estimation (JADE). AVAILABILITY: http://orclinux.creighton.edu/DGM/index.htm.