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At least 541 records · Page 30Linked to original sources

PubMed2003

DNannotator: Annotation software tool kit for regional genomic sequences.

Sequence annotation is essential for genomics-based research. Investigators of a specific genomic region who have developed abundant local discoveries such as genes and genetic markers, or have collected annotations from multiple resources, can be overwhelmed by the difficulty in creating local annotation and the complexity of integrating all the annotations. Presenting such integrated data in a form suitable for data mining and high-throughput experimental design is even more daunting. DNannotator, a web application, was designed to perform batch annotation on a sizeable genomic region. It takes annotation source data, such as SNPs, genes, primers, and so on, prepared by the end-user and/or a specified target of genomic DNA, and performs de novo annotation. DNannotator can also robustly migrate existing annotations in GenBank format from one sequence to another. Annotation results are provided in GenBank format and in tab-delimited text, which can be imported and managed in a database or spreadsheet and combined with existing annotation as desired. Graphic viewers, such as Genome Browser or Artemis, can display the annotation results. Reference data (reports on the process) facilitating the user's evaluation of annotation quality are optionally provided. DNannotator can be accessed at http://sky.bsd.uchicago.edu/DNannotator.htm.

Chromosomes, Human, Pair 13↗

PubMed2006

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

BACKGROUND: A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes), microdeletions, microduplications, and uniparental disomy. High density single nucleotide polymorphism (SNP) microarrays provide information on chromosomal copy number changes, as well as genotype (heterozygosity and homozygosity). SNP array studies generate multiple types of data for each SNP site, some with more than 100,000 SNPs represented on each array. The identification of different classes of anomalies within SNP data has been challenging. RESULTS: We have developed SNPscan, a web-accessible tool to analyze and visualize high density SNP data. It enables researchers (1) to visually and quantitatively assess the quality of user-generated SNP data relative to a benchmark data set derived from a control population, (2) to display SNP intensity and allelic call data in order to detect chromosomal copy number anomalies (duplications and deletions), (3) to display uniparental isodisomy based on loss of heterozygosity (LOH) across genomic regions, (4) to compare paired samples (e.g. tumor and normal), and (5) to generate a file type for viewing SNP data in the University of California, Santa Cruz (UCSC) Human Genome Browser. SNPscan accepts data exported from Affymetrix Copy Number Analysis Tool as its input. We validated SNPscan using data generated from patients with known deletions, duplications, and uniparental disomy. We also inspected previously generated SNP data from 90 apparently normal individuals from the Centre d'Etude du Polymorphisme Humain (CEPH) collection, and identified three cases of uniparental isodisomy, four females having an apparently mosaic X chromosome, two mislabelled SNP data sets, and one microdeletion on chromosome 2 with mosaicism from an apparently normal female. These previously unrecognized abnormalities were all detected using SNPscan. The microdeletion was independently confirmed by fluorescence in situ hybridization, and a region of homozygosity in a UPD case was confirmed by sequencing of genomic DNA. CONCLUSION: SNPscan is useful to identify chromosomal abnormalities based on SNP intensity (such as chromosomal copy number changes) and heterozygosity data (including regions of LOH and some cases of UPD). The program and source code are available at the SNPscan website http://pevsnerlab.kennedykrieger.org/snpscan.htm.

Base Sequence↗

PubMed1995

Technical report. Using a world wide web server as a local organizer for protein and DNA sequences.

We have used a local World Wide Web (WWW) server to organize protein and DNA sequences that are used frequently in our laboratory. WWW server programs are available for most computer platforms and are easily set up with minimal computer skills. This approach allows for the easy retrieval of sequence data, which can then be used as input for other analysis programs. This format is especially simple to use in conjunction with WWW database searches. The sequence files may be served to the "public" Internet or kept private by requiring a password for access. Other advantages are (i) sequences can be accessed from multiple computer platforms using the appropriate WWW-browser; (ii) files can be accessed remotely from any computer on the Internet; (iii) only a single sequence format is used, simplifying the updating and archiving of data; and (iv) links to remote files can also be served in addition to local files.

Amino Acid Sequence↗

PubMed2003

Patterns of searching for information on the World Wide Web: a pilot study.

The influences of task type on search of the World Wide Web using search engines without limitation of search domain were investigated. 9 graduate and undergraduate students studying psychology (1 woman and 8 men, M age=25.0 yr., SD=2.1) participated. Their performance to manipulate the search engines on a closed task with only one answer were compared with their performance on an open task with several possible answers. Analysis showed that the number of actions was larger for the closed task (M=91) than for the open task (M=46.1). Behaviors such as selection of keywords (averages were 7.9% of all actions for the closed task and 16.7% for the open task) and pressing of the browser's back button (averages were 40.3% of all actions for the closed task and 29.6% for the open task) were also different. On the other hand, behaviors such as selection of hyperlinks, pressing of the home button, and number of browsed pages were similar for both tasks. Search behaviors were influenced by task type when the students searched for information without limitation placed on the information sources.

Adult↗

PubMed2004

Visualization and analysis of microarray and gene ontology data with treemaps.

BACKGROUND: The increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the challenge of integrating experimental results with information resources. The use of Gene Ontology enables researchers to summarize results of quantitative analyses in this framework, but the limitations of typical browser presentation restrict data access. RESULTS: Here we describe extensions to the treemap design to visualize and query genome data. Treemaps are a space-filling visualization technique for hierarchical structures that show attributes of leaf nodes by size and color-coding. Treemaps enable users to rapidly compare sizes of nodes and sub-trees, and we use Gene Ontology categories, levels of RNA, and other quantitative attributes of DNA microarray experiments as examples. Our implementation of treemaps, Treemap 4.0, allows user-defined filtering to focus on the data of greatest interest, and these queried files can be exported for secondary analyses. Links to model system web pages from Treemap 4.0 enable users access to details about specific genes without leaving the query platform. CONCLUSIONS: Treemaps allow users to view and query the data from an experiment on a single computer monitor screen. Treemap 4.0 can be used to visualize various genome data, and is particularly useful for revealing patterns and details within complex data sets.

Animals↗

PubMed2006

BBP: Brucella genome annotation with literature mining and curation.

BACKGROUND: Brucella species are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Sequences of four Brucella genomes have been published, and various Brucella gene and genome data and analysis resources exist. A web gateway to integrate these resources will greatly facilitate Brucella research. Brucella genome data in current databases is largely derived from computational analysis without experimental validation typically found in peer-reviewed publications. It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation. It is further hypothesized that literature-based Brucella gene annotation would increase understanding of complicated Brucella pathogenesis mechanisms. RESULTS: The Brucella Bioinformatics Portal (BBP) is developed to integrate existing Brucella genome data and analysis tools with literature mining and curation. The BBP InterBru database and Brucella Genome Browser allow users to search and analyze genes of 4 currently available Brucella genomes and link to more than 20 existing databases and analysis programs. Brucella literature publications in PubMed are extracted and can be searched by a TextPresso-powered natural language processing method, a MeSH browser, a keywords search, and an automatic literature update service. To efficiently annotate Brucella genes using the large amount of literature publications, a literature mining and curation system coined Limix is developed to integrate computational literature mining methods with a PubSearch-powered manual curation and management system. The Limix system is used to quickly find and confirm 107 Brucella gene mutations including 75 genes shown to be essential for Brucella virulence. The 75 genes are further clustered using COG. In addition, 62 Brucella genetic interactions are extracted from literature publications. These results make possible more comprehensive investigation of Brucella pathogenesis. Other BBP features include publication email alert service, Brucella researchers' contact database, and discussion forum. CONCLUSION: BBP is a gateway for Brucella researchers to search, analyze, and curate Brucella genome data originated from public databases and literature. Brucella gene mutations and genetic interactions are annotated using Limix leading to better understanding of Brucella pathogenesis.

Algorithms↗

PubMed2003

Using a modified standard microscope to generate virtual slides.

A standard microscope was reconfigured as a virtual slide generator by adding a Prior Scientific H101 robotic stage with H29 controller and 0.1 microm linear scales and a Hitachi HV-C20 3CCD camera. Media Cybernetics Image Pro Plus version 4 (IP4) software controlled stage movement in the X-, Y-, and Z-axis, whereas a Media Cybernetics Pro-Series Capture Kit captured images at 640 x 480 pixels. Stage calibration, scanning algorithms, storage requirements, and viewing modes were standardized. IP4 was used to montage the captured images into a large virtual slide image that was subsequently saved in TIF or JPEG format. Virtual slides were viewed at the workstation using the IP4 viewer as well as Adobe Photoshop and Kodak Imaging. MGI Zoom Server delivered the virtual slides to the Internet, and MicroBrightField's Neuroinformatica viewing software provided a browser-based virtual microscope interface together with labeling tools for annotating virtual slides. The images were served from a Windows 2000 platform with 2 GB RAM, 500 GB of disk storage, and a 1.0 GHz P4 processor. To conserve disk space on the image server, TIF files were converted to the FlashPix (FPX) file format using a compression ratio of 10:1. By using 4x, 10x, 20x, and 40x objectives, very large gigapixel images of tissue whole-mounts and tissue arrays with high quality and morphologic detail are now being generated for teaching, publication, research, and morphometric analysis. Technical details and a demonstration of our system can be found on the Web at http://virtualmicroscope.osu.edu.

Anatomy, Cross-Sectional↗

PubMed2005

KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps.

The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of "omic" data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to a reaction are represented symbolically together with the symbols of the reaction and metabolites on metabolic pathway maps. Using quantitative values for transcripts and/or metabolites submitted by the user as Comma Separated Value-formatted text through the Internet, the KaPPA-View server inserts colored symbols corresponding to a defined metabolic process at that site on the maps and returns them to the user's browser. The server also provides information on transcripts and metabolites in pop-up windows. To demonstrate the process, we describe the dataset obtained for transgenic plants that overexpress the PAP1 gene encoding a MYB transcription factor on metabolic pathway maps. The presentation of data in this manner is useful for viewing metabolic data in a way that facilitates the discussion of gene function.

Computational Biology↗

PubMed1998

A VRML-based anatomical visualization tool for medical education.

The advent of the Virtual Reality Modeling Language (VRML) as a portable file format for describing three-dimensional (3-D) scenes has enabled researchers, educators, and students to share anatomical models on the World Wide Web (WWW). The implication for medical teaching is that students can interactively examine anatomical structures and their 3-D spatial relationships by using current personal computer (PC) technology. This paper describes the creation of 3-D anatomical models that are accessible on the WWW, using high-resolution middle-ear data as an example. The 3-D models are created by interactive segmentation of the source images (histological and MRI sections) and 3-D surface reconstruction. The resulting models are translated into VRML format. Section images can be superimposed on the model, allowing students to view a section in its 3-D context. To enhance the viewing of these scenes, a VRML browser was modified to support transparent rendering of surfaces. Finally, a WWW interface was designed to allow users to choose the model structures, section images, and associated viewing parameters to build their own 3-D scenes.

Education, Medical↗

PubMed2006

PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

We describe PReMod, a new database of genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes. The prediction algorithm, described previously in Blanchette et al. (2006) Genome Res., 16, 656-668, exploits the fact that many known CRMs are made of clusters of phylogenetically conserved and repeated transcription factors (TF) binding sites. Contrary to other existing databases, PReMod is not restricted to modules located proximal to genes, but in fact mostly contains distal predicted CRMs (pCRMs). Through its web interface, PReMod allows users to (i) identify pCRMs around a gene of interest; (ii) identify pCRMs that have binding sites for a given TF (or a set of TFs) or (iii) download the entire dataset for local analyses. Queries can also be refined by filtering for specific chromosomal regions, for specific regions relative to genes or for the presence of CpG islands. The output includes information about the binding sites predicted within the selected pCRMs, and a graphical display of their distribution within the pCRMs. It also provides a visual depiction of the chromosomal context of the selected pCRMs in terms of neighboring pCRMs and genes, all of which are linked to the UCSC Genome Browser and the NCBI. PReMod: http://genomequebec.mcgill.ca/PReMod.

Algorithms↗

PubMed1997

The Internet and randomised controlled trials.

Several factors constrain the implementation of Randomised Controlled Trials (RCTs). To obtain large sample sizes a multicentred multinational trial may be necessary or a long sampling period. The larger the trial the larger is the unit cost. To allow larger sample sizes, shorter sampling periods and lower unit costs, new methods are needed. The Internet and in particular the WWW provides such an opportunity. The WWW can provide global access, fast interaction and automation. A prototype Internet Trials Service (ITS) is currently being tested with a real international clinical trial (the Growth Restriction Intervention Trial--GRIT). The ITS is hosted on a Web server. It provides a series of HTML documents that describe the GRIT protocol. Registered centres may enter patients into the GRIT trial via ITS. Java applets are used to collect trial data before returning the study number and randomisation. ITS assumes all trial data will be intercepted by a sniffer. Therefore no information is sent that could specifically identify a patient, this must be sent later by more secure means. ITS assumes that trial centres can be spoofed. To authenticate the patients entered into the trial and the trial data sent, a regular audit report is sent to each centre by secure means for confirmation. By using Java, a full functional data entry system can be developed that runs locally within any Java enabled browser. It can perform data validation locally and also provide a sophisticated user interface.

Child Development↗

PubMed2000

Web-delivery of anatomy video clips using a CD-ROM.

Until recently, anatomists had no doubt that the teaching of anatomy had to include cadaver dissection. However, due to a changing academic environment as well as challenged financial institutional resources, computer-assisted instruction was introduced into medical curriculum in an attempt to reduce the cost and the time committed to cadaver dissection. Computer-assisted instruction included locally created or commercially available anatomy software, Internet sites, and databases of digital images of cadaveric structures such as the Virtual Human Project. However, until now, bandwidth limitations have not allowed effective visualization in real-time over the Internet of recorded videos or 3D animations reconstructed from a database. We describe how to successfully link and display large video clips stored on a CD-ROM in support of lectures saved in HTML format on the Internet. This process, described in its totality, allows students to access audiovisual files on a CD-ROM through the Internet, from any location, with either Macintosh or Windows computers, using the Netscape browser. This process allowed us to circumvent one of the most significant limitations of the computer-assisted instruction on the Internet by delivering full audio and visual information on demand, as it would happen in a traditional classroom.

Anatomy↗

PubMed2004

EnsMart: a generic system for fast and flexible access to biological data.

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets.

Animals↗

PubMed2006

Comparison of gene coverage of mouse oligonucleotide microarray platforms.

BACKGROUND: The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. RESULTS: A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis): Affymetrix430 2.0 (75.6%), ABI Genome Survey (81.24%), Agilent (79.33%), Codelink (78.09%), Sentrix (90.47%); and four array-ready oligosets: Sigma (47.95%), Operon v.3 (69.89%), Operon v.4 (84.03%), and MEEBO (84.03%). The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. CONCLUSION: The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here reveals that the commercial microarray Sentrix, which is based on the MEEBO public oligoset, showed the best mouse genome coverage currently available. We also suggest the creation of guidelines to standardize the minimum set of information that vendors should provide to allow researchers to accurately evaluate the advantages and disadvantages of using a given platform.

Animals↗

PubMed2000

Baby CareLink: using the internet and telemedicine to improve care for high-risk infants.

OBJECTIVE: To evaluate an Internet-based telemedicine program designed to reduce the costs of care, to provide enhanced medical, informational, and emotional support to families of very low birth weight (VLBW) infants during and after their neonatal intensive care unit (NICU) stay. BACKGROUND: Baby CareLink is a multifaceted telemedicine program that incorporates videoconferencing and World Wide Web (WWW) technologies to enhance interactions between families, staff, and community providers. The videoconferencing module allows virtual visits and distance learning from a family's home during an infant's hospitalization as well as virtual house calls and remote monitoring after discharge. Baby CareLink's WWW site contains information on issues that confront these families. In addition, its security architecture allows efficient and confidential sharing of patient-based data and communications among authorized hospital and community users. DESIGN/METHODS: A randomized trial of Baby CareLink was conducted in a cohort of VLBW infants born between November 1997 and April 1999. Eligible infants were randomized within 10 days of birth. Families of intervention group infants were given access to the Baby CareLink telemedicine application. A multimedia computer with WWW browser and videoconferencing equipment was installed in their home within 3 weeks of birth. The control group received care as usually practiced in this NICU. Quality of care was assessed using a standardized family satisfaction survey administered after discharge. In addition, the effect of Baby CareLink on hospital length of stay as well as family visitation and interactions with infant and staff were measured. RESULTS: Of the 176 VLBW infants admitted during the study period, 30 control and 26 study patients were enrolled. The groups were similar in patient and family characteristics as well as rates of inpatient morbidity. The CareLink group reported higher overall quality of care. Families in the CareLink group reported significantly fewer problems with the overall quality of care received by their family (mean problem score: 3% vs 13%). In addition, CareLink families also reported greater satisfaction with the unit's physical environment and visitation policies (mean problem score: 13% vs 50%). The frequency of family visits, telephone calls to the NICU, and holding of the infant did not differ between groups. The duration of hospitalization until ultimate discharge home was similar in the 2 groups (68.5 +/- 28.3 vs 70.6 +/- 35.6 days). Among infants born weighing <1000 g (n = 31) there was a tendency toward shorter lengths of stay (77.4 +/- 26.2 vs 93.1 +/- 35.6 days). All infants in the CareLink group were discharged directly to home whereas 6/30 (20%) of control infants were transferred to community hospitals before ultimate discharge home. CONCLUSIONS: CareLink significantly improves family satisfaction with inpatient VLBW care and definitively lowers costs associated with hospital to hospital transfer. Our data suggest the use of telemedicine and the Internet support the educational and emotional needs of families facilitating earlier discharge to home of VLBW infants. We believe that further extension of the Baby CareLink model to the postdischarge period will significantly improve the coordination and efficiency of care.

Aftercare↗

PubMed2004

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs). zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, in which functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser, allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.

Animals↗

PubMed2002

Web-based experiments controlled by JavaScript: an example from probability learning.

JavaScript programs can be used to control Web experiments. This technique is illustrated by an experiment that tested the effects of advice on performance in the classic probability-learning paradigm. Previous research reported that people tested via the Web or in the lab tended to match the probabilities of their responses to the probabilities that those responses would be reinforced. The optimal strategy, however, is to consistently choose the more frequent event; probability matching produces suboptimal performance. We investigated manipulations we reasoned should improve performance. A horse race scenario in which participants predicted the winner in each of a series of races between two horses was compared with an abstract scenario used previously. Ten groups of learners received different amounts of advice, including all combinations of (1) explicit instructions concerning the optimal strategy, (2) explicit instructions concerning a monetary sum to maximize, and (3) accurate information concerning the probabilities of events. The results showed minimal effects of horse race versus abstract scenario. Both advice concerning the optimal strategy and probability information contributed significantly to performance in the task. This paper includes a brief tutorial on JavaScript, explaining with simple examples how to assemble a browser-based experiment.

Computer-Assisted Instruction↗

PubMed1994

OncoLink: a multimedia oncology information resource on the Internet.

This paper describes OncoLink, the first multimedia World-Wide-Web (WWW) and gopher server focusing on cancer information for both the health care professional and the patient. OncoLink provides an internetworked hypertext and multimedia resource linking people, computers and information together in an easy to use fashion. Our objective in developing OncoLink is to provide comprehensive and timely information about many aspects of oncology for both patients and healthcare providers. Specifically, OncoLink's purposes are: (1) the rapid dissemination of information relevant to treatment of cancer and concomitant problems; (2) education of health care personnel (at all levels) in the field; (3) education of patients and families of patients who have cancer; (4) posting of clinical trials and eligibility criteria; (5) the rapid collection and dissemination of quality, peer-reviewed information pertinent to oncology in general and specific subspecialties; (6) provide a well-organized, frequently updated hypertext system to access other quality cancer information resources on the Internet. OncoLink attempts to provide one-stop shopping for the patient, healthcare provider, researcher or Internet browser searching for cancer-related information. Since its inception on March 7, 1994, OncoLink has averaged more than 36,000 accesses per month from around the world. While also accessible by text-based gopher servers, preliminary observations infer increased use of multimedia and hypertext documents over traditional text-only resources. From the large following of users, it is clear that electronic dissemination of high quality, peer-reviewed cancer information is very popular. We conclude OncoLink is both useful and has wide interest in the international community.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Communication Networks↗