The Mouse Gene Expression Database (GXD)

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD’s utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatic s.jax.org/ or directly at http://www.informatics.jax.org/me nus/expression_menu.shtml.

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm

The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list of structurally similar proteins along with their structure alignments. Using CE, structure–structure alignments can provide insights into biological function. When a protein of known function is shown to be structurally similar to a protein of unknown function, a relationship might be inferred; a relationship not necessarily detectable from sequence comparison alone. Establishing structure–structure relationships in this way is of great importance as we enter an era of structural genomics where there is a likelihood of an increasing number of structures with unknown functions being determined. Thus the CE database is an example of a useful tool in the annotation of protein structures of unknown function. Comparisons can be performed on the complete PDB or on a structurally representative subset of proteins. The source protein(s) can be from the PDB (updated monthly) or uploaded by the user. CE provides sequence alignments resulting from structural alignments and Cartesian coordinates for the aligned structures, which may be analyzed using the supplied Compare3D Java applet, or downloaded for further local analysis. Searches can be run from the CE web site, http://cl.sdsc.edu/ce.html, or the database and software downloaded from the site for local use.

rrndb: the Ribosomal RNA Operon Copy Number Database

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu.

Mendel, a database of nomenclature for sequenced plant genes

The Mendel database contains names for plant-wide families of sequenced plant genes. The names have either been approved by the Commission on Plant Gene Nomenclature (CPGN), an organization of the International Society for Plant Molecular Biology (ISPMB), or are identified as provisional or temporary names. Mendel also identifies the corresponding genes in individual species of plants. Mendel can be searched through the mirror sites at Cornell (http://genome.cornell.edu/cgi-bin/WebAce/webace?db=mendel) and Stanford (http://genome-www.stanford.edu/Mendel/). In addition, parts of Mendel can be downloaded from the CPGN Web site (http://mbclserver.rutgers.edu/CPGN/).

The Molecular Biology Database Collection: an updated compilation of biological database resources

The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www.nar.oupjournals.org.

A library-based bioinformatics services program*

Support for molecular biology researchers has been limited to traditional library resources and services in most academic health sciences libraries. The University of Washington Health Sciences Libraries have been providing specialized services to this user community since 1995. The library recruited a Ph.D. biologist to assess the molecular biological information needs of researchers and design strategies to enhance library resources and services. A survey of laboratory research groups identified areas of greatest need and led to the development of a three-pronged program: consultation, education, and resource development. Outcomes of this program include bioinformatics consultation services, library-based and graduate level courses, networking of sequence analysis tools, and a biological research Web site. Bioinformatics clients are drawn from diverse departments and include clinical researchers in need of tools that are not readily available outside of basic sciences laboratories. Evaluation and usage statistics indicate that researchers, regardless of departmental affiliation or position, require support to access molecular biology and genetics resources. Centralizing such services in the library is a natural synergy of interests and enhances the provision of traditional library resources. Successful implementation of a library-based bioinformatics program requires both subject-specific and library and information technology expertise.

The Research Funding Service: a model for expanded library services

Traditionally, libraries have provided a modest amount of information about grants and funding opportunities to researchers in need of research funding. Ten years ago, the University of Washington (UW) Health Sciences Libraries and Information Center joined in a cooperative effort with the School of Medicine to develop a complete, library-based grant and funding service for health sciences researchers called the Research Funding Service. The library provided space, access to the library collection, equipment, and electronic resources, and the School of Medicine funded staff and operations. The range of services now includes individual consultation appointments, an extensive Web site, classes on funding database searching and writing grant applications, a discussion series that frequently hosts guest speakers, a monthly newsletter with funding opportunities of interest to the six health sciences schools, extensive files on funding sources, and referral services.

Experiences with free and open courses using on-line multimedia resources

This paper analyzes the learning experiences and opinions obtained from a group of undergraduate students in their interaction with several on-line multimedia resources included in a free on-line course about Computer Networks. These new educational resources employed are based on the Web2.0 approach such as blogs, videos and virtual labs which have been added in a web-site for distance self-learning.

Open educational resources: the role of OCW, blogs and videos in computer network classrooms

This paper analyzes the learning experiences and opinions obtained from a group of undergraduate students in their interaction with several on-line multimedia resources included in a free on-line course about Computer Networks. These new educational resources employed are based on the Web 2.0 approach such as blogs, videos and virtual labs which have been added in a web-site for distance self-learning.

ConfChem Conference on A Virtual Colloquium to Sustain and Celebrate IYC 2011 Initiatives in Global Chemical Education—The Global Experiment of the IYC2011: Creating Online Communities for Education and Science

The Global Experiment, Water: A Chemical Solution, was one of the flagship activities of the International Year of Chemistry (IYC). During the virtual colloquium of the spring 2012 online ConfChem conference, the main results of this year-long experiment were presented and discussed online for a week. Some of the main conclusions of the virtual conversations relate to the benefits of creating online communities of people sharing similar interests, the use of online educational platforms to gather massive amounts of data, and specific questions about the development of this IYC initiative. The activities of the global water experiment (GWE) were designed by a team of experts and the protocols are available online on the GWE Web site. The results were shown in one interactive world map that allowed students to learn about data visualization, validation, and interpretation. The feedback obtained from the participants of the GWE and later by the contributors of the virtual colloquium was very positive. Many participants asked specific and technical questions about the development of this experiment, while others excitedly endorsed the convenience of these large open-access activities to promote chemistry worldwide. The estimate is that over 2 million people took part in the GWE during the IYC. This communication summarizes one of the invited papers to the ConfChem online conference: A Virtual Colloquium to Sustain and Celebrate IYC 2011 Initiatives in Global Chemical Education, held from May 18 to June 29, 2012 and hosted by the ACS DivCHED Committee on Computers in Chemical Education and the IUPAC Committee on Chemistry Education.

Charles Town, South Carolina: with a chart of the bars & harbour

by R. Cowley.

Rock map of the Yellow River (Huang He) expedition, China, 1925-1927 : Sheet 2

This layer is part of a set of georeferenced, raster images of the manuscript, paper map set entitled: Ch'ing-Hai upper Yellow River expedition : Rock and Simpson, 1925-27, [cartography by J.F. Rock]. Scale 1:250,000. This layer image is of Sheet II [of 10] covering a portion of the Yellow River (Huang He) region in eastern Qinghai Sheng and southern Gansu Sheng, China. The map set details the route and surrounding environs of the Arnold Arboretum's "Western China" expedition led by Joseph Rock, 1924-1927. The set covers a portion of the Yellow River (Huang He) region in south central China (Qinghai, Gansu, and Sichuan shengs (a portion of historic Tibet)). It shows features, labeled variously in English, Chinese, Wade-Giles transliteration, and Tibetan, including: rivers, streams, lakes, mountains, gorges, valleys, plateaus, plains, cities, towns, villages, provincial capitals, county seats, passes, monasteries, ruin sites, native tribe locations, and more. Relief is shown by hachures, spot heights, and landform drawings. The original manuscript map set is part of the Harvard College Library, Harvard Map Collection. "Joseph Rock traced his travels for the [Arnold] Arboretum's [Western China] 1924-1927 expedition in a colorful, hand-drawn map entitled 'Ch'ing-Hai upper Yellow River expedition.' The pen-and-ink drawing was made on ten sheets that when joined form a single, irregularly-shaped map, approximately six by eight feet in size. The individual sheets are numbered, using roman numerals; on sheet VII is a second title, 'Choni Territory, Upper and Lower T'ieh-Pu country and route to Sung-Pan, J. F. Rock, 1925-1927.' Topographical and other features are identified using a combination of English, Chinese characters, Wade-Giles transliterations and Tibetan script. Rock's attractive cursive style and use of hachures, spot heights, and landform drawings to depict relief add character to the map." -- Text from the Arnold Arboretum Web site.

Rock map of the Yellow River (Huang He) expedition, China, 1925-1927 : Sheet 3

This layer is part of a set of georeferenced, raster images of the manuscript, paper map set entitled: Ch'ing-Hai upper Yellow River expedition : Rock and Simpson, 1925-27, [cartography by J.F. Rock]. Scale 1:250,000. This layer image is of Sheet III [of 10] covering a portion of the Yellow River (Huang He) region in eastern Qinghai Sheng and southern Gansu Sheng, China. The map set details the route and surrounding environs of the Arnold Arboretum's "Western China" expedition led by Joseph Rock, 1924-1927. The set covers a portion of the Yellow River (Huang He) region in south central China (Qinghai, Gansu, and Sichuan shengs (a portion of historic Tibet)). It shows features, labeled variously in English, Chinese, Wade-Giles transliteration, and Tibetan, including: rivers, streams, lakes, mountains, gorges, valleys, plateaus, plains, cities, towns, villages, provincial capitals, county seats, passes, monasteries, ruin sites, native tribe locations, and more. Relief is shown by hachures, spot heights, and landform drawings. The original manuscript map set is part of the Harvard College Library, Harvard Map Collection. "Joseph Rock traced his travels for the [Arnold] Arboretum's [Western China] 1924-1927 expedition in a colorful, hand-drawn map entitled 'Ch'ing-Hai upper Yellow River expedition.' The pen-and-ink drawing was made on ten sheets that when joined form a single, irregularly-shaped map, approximately six by eight feet in size. The individual sheets are numbered, using roman numerals; on sheet VII is a second title, 'Choni Territory, Upper and Lower T'ieh-Pu country and route to Sung-Pan, J. F. Rock, 1925-1927.' Topographical and other features are identified using a combination of English, Chinese characters, Wade-Giles transliterations and Tibetan script. Rock's attractive cursive style and use of hachures, spot heights, and landform drawings to depict relief add character to the map." -- Text from the Arnold Arboretum Web site.

Rock map of the Yellow River (Huang He) expedition, China, 1925-1927 : Sheet 4

This layer is part of a set of georeferenced, raster images of the manuscript, paper map set entitled: Ch'ing-Hai upper Yellow River expedition : Rock and Simpson, 1925-27, [cartography by J.F. Rock]. Scale 1:250,000. This layer image is of Sheet IV [of 10] covering a portion of the Yellow River (Huang He) region in eastern Qinghai Sheng, China. The map set details the route and surrounding environs of the Arnold Arboretum's "Western China" expedition led by Joseph Rock, 1924-1927. The set covers a portion of the Yellow River (Huang He) region in south central China (Qinghai, Gansu, and Sichuan shengs (a portion of historic Tibet)). It shows features, labeled variously in English, Chinese, Wade-Giles transliteration, and Tibetan, including: rivers, streams, lakes, mountains, gorges, valleys, plateaus, plains, cities, towns, villages, provincial capitals, county seats, passes, monasteries, ruin sites, native tribe locations, and more. Relief is shown by hachures, spot heights, and landform drawings. The original manuscript map set is part of the Harvard College Library, Harvard Map Collection. "Joseph Rock traced his travels for the [Arnold] Arboretum's [Western China] 1924-1927 expedition in a colorful, hand-drawn map entitled 'Ch'ing-Hai upper Yellow River expedition.' The pen-and-ink drawing was made on ten sheets that when joined form a single, irregularly-shaped map, approximately six by eight feet in size. The individual sheets are numbered, using roman numerals; on sheet VII is a second title, 'Choni Territory, Upper and Lower T'ieh-Pu country and route to Sung-Pan, J. F. Rock, 1925-1927.' Topographical and other features are identified using a combination of English, Chinese characters, Wade-Giles transliterations and Tibetan script. Rock's attractive cursive style and use of hachures, spot heights, and landform drawings to depict relief add character to the map." -- Text from the Arnold Arboretum Web site.

Rock map of the Yellow River (Huang He) expedition, China, 1925-1927 : Sheet 9

This layer is part of a set of georeferenced, raster images of the manuscript, paper map set entitled: Ch'ing-Hai upper Yellow River expedition : Rock and Simpson, 1925-27, [cartography by J.F. Rock]. Scale 1:250,000. This layer image is of Sheet IX [of 10] covering a portion of the Yellow River (Huang He) region in southern Gansu Sheng and northwestern Sichuan Sheng, China, including parts of Baishui Jiang and Pai Ho (Gar He). The map set details the route and surrounding environs of the Arnold Arboretum's "Western China" expedition led by Joseph Rock, 1924-1927. The set covers a portion of the Yellow River (Huang He) region in south central China (Qinghai, Gansu, and Sichuan shengs (a portion of historic Tibet)). It shows features, labeled variously in English, Chinese, Wade-Giles transliteration, and Tibetan, including: rivers, streams, lakes, mountains, gorges, valleys, plateaus, plains, cities, towns, villages, provincial capitals, county seats, passes, monasteries, ruin sites, native tribe locations, and more. Relief is shown by hachures, spot heights, and landform drawings. The original manuscript map set is part of the Harvard College Library, Harvard Map Collection. "Joseph Rock traced his travels for the [Arnold] Arboretum's [Western China] 1924-1927 expedition in a colorful, hand-drawn map entitled 'Ch'ing-Hai upper Yellow River expedition.' The pen-and-ink drawing was made on ten sheets that when joined form a single, irregularly-shaped map, approximately six by eight feet in size. The individual sheets are numbered, using roman numerals; on sheet VII is a second title, 'Choni Territory, Upper and Lower T'ieh-Pu country and route to Sung-Pan, J. F. Rock, 1925-1927.' Topographical and other features are identified using a combination of English, Chinese characters, Wade-Giles transliterations and Tibetan script. Rock's attractive cursive style and use of hachures, spot heights, and landform drawings to depict relief add character to the map." -- Text from the Arnold Arboretum Web site.