One fifth of Americans smoke; many have no plans to quit. Motivational Interviewing (MI) is an effective approach to intervention with precontemplative smokers, yet a substantial number of healthcare practitioners lack training in this approach. Two interactive online tutorials were developed to teach practitioners to deliver brief tobacco cessation interventions grounded in the MI approach. The tutorials emphasized the unique aspects of working with precontemplative smokers, incorporating audio and video examples of best practices, interactive exercises, targeted feedback, and practice opportunities. One hundred and fifty-two healthcare providers-in-training were randomly assigned to use the online tutorials or to read training material that was matched for content. A virtual standardized patient evaluation was given before and after the training. Both groups improved their scores from pre- to posttest; however, the tutorial group scored significantly better than the reading group at posttest. The results of this study demonstrate the promise of interactive online tutorials as an efficient and effective way to deliver clinical education.
Internet; Medical Education; Smoking; Tobacco; Motivation Techniques
Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is ‘Using the MaizeGDB Genome Browser’, which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser.
Database URL: http://www.maizegdb.org/
Web services have become widely used in bioinformatics analysis, but there exist incompatibilities in interfaces and data types, which prevent users from making full use of a combination of these services. Therefore, we have developed the TogoWS service to provide an integrated interface with advanced features. In the TogoWS REST (REpresentative State Transfer) API (application programming interface), we introduce a unified access method for major database resources through intuitive URIs that can be used to search, retrieve, parse and convert the database entries. The TogoWS SOAP API resolves compatibility issues found on the server and client-side SOAP implementations. The TogoWS service is freely available at: http://togows.dbcls.jp/.
This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB.
Database URL: http://www.pdbj.org/
We have witnessed a rapid increase in the use of Web-based 'collaborationware' in recent years. These Web 2.0 applications, particularly wikis, blogs and podcasts, have been increasingly adopted by many online health-related professional and educational services. Because of their ease of use and rapidity of deployment, they offer the opportunity for powerful information sharing and ease of collaboration. Wikis are Web sites that can be edited by anyone who has access to them. The word 'blog' is a contraction of 'Web Log' – an online Web journal that can offer a resource rich multimedia environment. Podcasts are repositories of audio and video materials that can be "pushed" to subscribers, even without user intervention. These audio and video files can be downloaded to portable media players that can be taken anywhere, providing the potential for "anytime, anywhere" learning experiences (mobile learning).
Wikis, blogs and podcasts are all relatively easy to use, which partly accounts for their proliferation. The fact that there are many free and Open Source versions of these tools may also be responsible for their explosive growth. Thus it would be relatively easy to implement any or all within a Health Professions' Educational Environment. Paradoxically, some of their disadvantages also relate to their openness and ease of use. With virtually anybody able to alter, edit or otherwise contribute to the collaborative Web pages, it can be problematic to gauge the reliability and accuracy of such resources. While arguably, the very process of collaboration leads to a Darwinian type 'survival of the fittest' content within a Web page, the veracity of these resources can be assured through careful monitoring, moderation, and operation of the collaborationware in a closed and secure digital environment. Empirical research is still needed to build our pedagogic evidence base about the different aspects of these tools in the context of medical/health education.
Summary and conclusion
If effectively deployed, wikis, blogs and podcasts could offer a way to enhance students', clinicians' and patients' learning experiences, and deepen levels of learners' engagement and collaboration within digital learning environments. Therefore, research should be conducted to determine the best ways to integrate these tools into existing e-Learning programmes for students, health professionals and patients, taking into account the different, but also overlapping, needs of these three audience classes and the opportunities of virtual collaboration between them. Of particular importance is research into novel integrative applications, to serve as the "glue" to bind the different forms of Web-based collaborationware synergistically in order to provide a coherent wholesome learning experience.
One of the drawbacks of studying pathology in the second year of medical school in a classroom setting is the relatively limited exposure to patient encounters/clinical rotations, making it difficult to understand and fully appreciate the significance of the course material, specifically the molecular and tissue aspects of disease. In this study, we determined if case vignettes incorporating pathologist-clinician encounters with whole slide imaging (WSI) and narrated/annotated videos of whole slide (WS) scans in addition to clinical data improved student understanding of pathologic disease processes.
Materials and Methods:
Case vignettes were created for several genitourinary disease processes that utilized clinical data including narratives of pathologist-clinician encounters, WSI, and annotated video tutorials of WS scans (designed to simulate “double-heading”). The students were encouraged to view the virtual slide first, with the video tutorials being provided to offer additional assistance. The case vignettes were created to be interactive with a detailed explanation of each correct and incorrect question choice. The cases were made available to all second year medical students via a website and could be viewed only after completing a 10 question pre-test. A post-test could be completed after viewing all cases followed by a brief satisfaction survey.
Ninety-six students completed the pre-test with an average score of 7.7/10. Fifty-seven students completed the post-test with an average score of 9.4/10. Thirty-six students completed the satisfaction survey. 94% agreed or strongly agreed that this was a useful exercise and 91% felt that it helped them better understand the topics.
The development of interactive case vignettes incorporating simulated pathologist-clinician encounters with WSI and video tutorials of WS scans helps to improve student enthusiasm to learn and grasp pathologic aspects of disease processes that lead to clinical therapeutic decision making.
Education; whole slide imaging; medical student
Summary: Computational methods designed to discover transcription factor binding sites in DNA sequences often have a tendency to make a lot of false predictions. One way to improve accuracy in motif discovery is to rely on positional priors to focus the search to parts of a sequence that are considered more likely to contain functional binding sites. We present here a program called PriorsEditor that can be used to create such positional priors tracks based on a combination of several features, including phylogenetic conservation, nucleosome occupancy, histone modifications, physical properties of the DNA helix and many more.
Availability: PriorsEditor is available as a web start application and downloadable archive from http://tare.medisin.ntnu.no/priorseditor (requires Java 1.6). The web site also provides tutorials, screenshots and example protocol scripts.
Objective: We describe a working software technology that enables educators to incorporate their expertise and teaching style into highly interactive and Socratic educational material for distribution on the world wide web.Materials/Methods: A graphically oriented interactive authoring system was developed to enable the computer novice to create and store within a database his or her domain expertise in the form of electronic knowledge. The authoring system supports and facilitates the input and integration of several types of content, including free-form, stylized text, miniature and full-sized images, audio, and interactive questions with immediate feedback. The system enables the choreography and sequencing of these entities for display within a web page as well as the sequencing of entire web pages within a case-based or thematic presentation. Images or segments of text can be hyperlinked with point-and-click to other entities such as adjunctive web pages, audio, or other images, cases, or electronic chapters. Miniature (thumbnail) images are automatically linked to their full-sized counterparts. The authoring system contains a graphically oriented word processor, an image editor, and capabilities to automatically invoke and use external image-editing software such as Photoshop. The system works in both local area network (LAN) and internet-centric environments. An internal metalanguage (invisible to the author but stored with the content) was invented to represent the choreographic directives that specify the interactive delivery of the content on the world wide web. A database schema was developed to objectify and store both this electronic knowledge and its associated choreographic metalanguage. A database engine was combined with page-rendering algorithms in order to retrieve content from the database and deliver it on the web in a Socratic style, assess the recipient’s current fund of knowledge, and provide immediate feedback, thus stimulating in-person interaction with a human expert.Results: This technology enables the educator to choreograph a stylized, interactive delivery of his or her message using multimedia components assembled in virtually any order, spanning any number of thus exercise precise influence on specific learning objectives, embody his or her personal teaching style within the content, and ultimately enhance its educational impact.Conclusion: The described technology amplifies the efforts of the educator and provides a more dynamic and enriching learning environment for web-based education.
The advance of web-based technology has stimulated innovation in education. This paper discusses the development and evaluation of an online multimedia resource for undergraduate-level behavioral neuroscience education. This resource surveys four major subject areas: language, attention and perception, thinking, and autism. It employs audio and video streaming, online demonstration experiments, computer simulation, and internet links. This online resource has two distinct advantages over a paper textbook. First, a considerable proportion of the content is conveyed using multimedia, thus making the learning experience more vivid and dynamic. Second, its interactive components provide opportunities for students to participate in the various experimental tasks introduced in the text and to compare their own performance with those of others. This hands-on experience not only enables students to gain in-depth procedural knowledge of the tasks but also has positive effects on their motivation. Feedback from three undergraduate classes that used this resource as supplementary material showed that students were highly positive about its pedagogical values. This free resource is available on the web at http://psych.rice.edu/mmtbn/.
multimedia; streaming audio; streaming video; online demonstration; computer simulation; aphasia; parallel distributed processing (PDP); visual search; autism
Neuronal morphology affects network connectivity, plasticity, and information processing. Uncovering the design principles and functional consequences of dendritic and axonal shape necessitates quantitative analysis and computational modeling of detailed experimental data. Digital reconstructions provide the required neuromorphological descriptions in a parsimonious, comprehensive, and reliable numerical format. NeuroMorpho.Org is the largest web-accessible repository service for digitally reconstructed neurons and one of the integrated resources in the Neuroscience Information Framework (NIF). Here we describe the NeuroMorpho.Org approach as an exemplary experience in designing, creating, populating, and curating a neuroscience digital resource. The simple three-tier architecture of NeuroMorpho.Org (web client, web server, and relational database) encompasses all necessary elements to support a large-scale, integrate-able repository. The data content, while heterogeneous in scientific scope and experimental origin, is unified in format and presentation by an in house standardization protocol. The server application (MRALD) is secure, customizable, and developer-friendly. Centralized processing and expert annotation yields a comprehensive set of metadata that enriches and complements the raw data. The thoroughly tested interface design allows for optimal and effective data search and retrieval. Availability of data in both original and standardized formats ensures compatibility with existing resources and fosters further tool development. Other key functions enable extensive exploration and discovery, including 3D and interactive visualization of branching, frequently measured morphometrics, and reciprocal links to the original PubMed publications. The integration of NeuroMorpho.Org with version-1 of the NIF (NIFv1) provides the opportunity to access morphological data in the context of other relevant resources and diverse subdomains of neuroscience, opening exciting new possibilities in data mining and knowledge discovery. The outcome of such coordination is the rapid and powerful advancement of neuroscience research at both the conceptual and technological level.
Neuronal morphology; Digital reconstruction; Data sharing; Neuroscience Information Framework; Axonal arbors; Dendritic trees
We have developed a computer-based interactive tutorial which integrates still frame images of melanoma from a videodisc with text and graphics from a personal computer. The tutorial utilizes some of the features of the IBM InfoWindows environment. The content has been developed by dermatology educators to emphasize the possibility of diagnosis of early melanoma by non-dermatologists. The process was intended to test the feasibility of medical educators authoring an interactive video lesson without prior training in an authoring software system.
The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe “Genomer,” a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs.
Motivation: Meta-analysis of large gene expression datasets obtained from public repositories requires consistently annotated data. Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline.
Results: We present MageComet, a web application for biologists and annotators that facilitates the re-annotation of gene expression experiments in MAGE-TAB format. It incorporates data mining, automatic annotation, use of ontologies and data validation to improve the consistency and quality of experimental meta-data from the ArrayExpress Repository.
Availability and implementation: Source and tutorials for MageComet are openly available at goo.gl/8LQPR under the GNU GPL v3 licenses. An implementation can be found at goo.gl/IdCuA
email@example.com or firstname.lastname@example.org
OBJECTIVE: To describe a Web-based guideline tutorial system and evaluate its features. METHODS: A Web-based tutorial system called SAGE (Self-study Acceleration with Graphic Evidence) was constructed to teach knowledge important for care after myocardial infarction. SAGE features a pretest, followed by an overview that coordinates studying resources for a set of learning objectives. Resources include pretest answers, guideline passages, and graphical presentations of clinical trial results. Data on the use of SAGE was obtained from 79 residents participating in a larger trial. Linear regression was used to correlate the amount learned with resource-use, and resource-use with user characteristics. RESULTS: On average, users accessed less than half of the guideline passages and very little of the graphic evidence. Greater use of guideline passages was correlated with greater immediate learning, but use of graphic evidence was not. CONCLUSIONS: Further research is needed to motivate more thorough self-study and to integrate clinical trial evidence with guideline-based education.
As part of the required curriculum for medical students, we devised a literature-searching practicum that has been used for two years. In both years, we stressed going beyond the skills needed for using a particular searching program, towards a more conceptual approach to information searching. In the first year, the practicum was taught in a traditional lecture/hands-on format. In the second year, the lecture was replaced by a World Wide Web-based tutorial (http:@www.welch.jhu.edu/Education/tutorials/pra cticum.html). To our knowledge, this is the first Web-based resource intended to teach students about appropriate use of search technology. Comparison of student evaluations showed no difference in attitude toward the two versions of the practicum, and observation of student performance suggested similar levels of proficiency. We conclude that placing these educational materials on the Web (1) makes us practice what we preach; (2) is as effective as traditional teaching methods; and (3) gives students a resource for reinforcement learning.
In response to the lack of readily available multimedia rich medical knowledge sources to support medical education and patient care, we designed and implemented a web-based video publishing platform. In order to promote the development of high-quality, up-to-date educational content, we have devised a scalable structure that allows online submissions and continuous updating of video and accompanying textual descriptions. Our goal is to enable experts in varied medical domains to collaborate in the construction of a video library using an intuitive web-based interface. Neurologists at Stanford built a well-annotated neurology video collection that initially emphasized childhood and adult movement disorders. The collection may be accessed either as a stand-alone resource or as part of the Stanford Skolar MD, an integrated online medical knowledge provider. This manuscript discusses the design framework and implementation details of structured media content development. We present examples illustrating media data collection, content indexing using UMLS concepts, media storage, and web presentation.
Knowledge of quality measures in endoscopy among trainees is unknown.
To assess knowledge of endoscopy-related quality indicators among U.S. trainees and determine whether it improves with a Web-based intervention.
Randomized, controlled study.
This study involved trainees identified from the American Society for Gastrointestinal Endoscopy membership database.
Participants were invited to complete an 18-question online test. Respondents were randomized to receive a Web-based tutorial (intervention) or not. The test was readministered 6 weeks after randomization to determine the intervention’s impact.
Main Outcome Measurements
Baseline knowledge of endoscopy-related quality indicators and impact of the tutorial.
A total of 347 of 1220 trainees (28%) completed the test; the mean percentage of correct responses was 55%. For screening colonoscopy, 44% knew the adenoma detection rate benchmark, 42% identified the cecal intubation rate goal, and 74% knew the recommended minimum withdrawal time. A total of 208 of 347 trainees (59%) completed the second test; baseline scores were similar for the tutorial (n = 106) and no tutorial (n = 102) groups (56.4% vs 56.9%, respectively). Scores improved after intervention for the tutorial group (65%, P = .003) but remained unchanged in the no tutorial group. On multivariate analysis, each additional year in training (odds ratio [OR] 2.3; 95% confidence interval [CI], 1.5–3.4), training at an academic institution (OR 2.6; 95% CI, 1.1–6.3), and receiving the tutorial (OR 3.2; 95% CI, 1.7–5.9) were associated with scores in the upper tertile.
Low response rate.
Knowledge of endoscopy-related quality performance measures is low among trainees but can improve with a Web-based tutorial. Gastroenterology training programs may need to incorporate a formal didactic curriculum to supplement practice-based learning of quality standards in endoscopy. (Gastrointest Endosc 2012;76:100–6.)
The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists.
The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/.
With FAME, we present the community with an open source, user-friendly, web-based "one stop shop" for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike.
Objective: Early intervention can significantly improve long-term outcomes for children with autism. Unfortunately, many children do not receive early intervention services due to a critical shortage of trained professionals in this area. To bridge this gap, we evaluated a Web-based parent training tutorial (Enhancing Interactions), based on evidence-based practices and utilizing the Web-based platform to maximize learning. Methods: Twenty-three parents with a child between 18 months and 6 years with an autism spectrum disorder participated. Pre- and posttest scores of parents' knowledge were used to evaluate tutorial effectiveness. The system usability scale (SUS) evaluated technical user-friendliness and the user satisfaction questionnaire (USQ), gauged satisfaction with content. Results: The mean number of correct items on the posttest significantly increased, from 12.6 to 20.4, p<0.001. The mean SUS score was 85 (standard deviation=17), corresponding to a score of “excellent.” All participants found the tutorial user friendly, well integrated, and 96% (all but one participant) thought it was easy to use, felt confident using the technical features, and would use a tutorial like this again. On the USQ, all participants found that the tutorial was well organized, clearly presented, and easy to understand; that it increased their knowledge about communicating with their child; and that they felt capable of applying these techniques with their child. Conclusions: The tutorial appears effective in increasing parents' knowledge with high user satisfaction.
distance learning; telehealth; telepsychiatry
The Laminin(LM)-database, hosted at http://www.lm.lncc.br, is the first database focusing a non-collagenous extracellular matrix protein family, the LMs. Part of the knowledge available in this website is automatically retrieved, whereas a significant amount of information is curated and annotated, thus placing LM-database beyond a simple repository of data. In its home page, an overview of the rationale for the database is seen and readers can access a tutorial to facilitate navigation in the website, which in turn is presented with tabs subdivided into LMs, receptors, extracellular binding and other related proteins. Each tab opens into a given LM or LM-related molecule, where the reader finds a series of further tabs for ‘protein’, ‘gene structure’, ‘gene expression’ and ‘tissue distribution’ and ‘therapy’. Data are separated as a function of species, comprising Homo sapiens, Mus musculus and Rattus novergicus. Furthermore, there is specific tab displaying the LM nomenclatures. In another tab, a direct link to PubMed, which can be then consulted in a specific way, in terms of the biological functions of each molecule, knockout animals and genetic diseases, immune response and lymphomas/leukemias. LM-database will hopefully be a relevant tool for retrieving information concerning LMs in health and disease, particularly regarding the hemopoietic system.
This paper describes some of the design criteria for a facility to support problem-based tutorials, known as the Computer-Mediated Tutorial Laboratory (CMTL). In the CMTL, a networked workstation will be provided for the tutor and each of the students. The tutor's workstation will be connected to a projection system, permitting the entire group to view the tutor's screen. The software used in the CMTL will have three components: a Patient Simulation Stack (PSS), the group/student Tutorial Stacks (TSs) and the network communication interface. The PSS represents a clinical problem; it is designed to realistically simulate an encounter with an actual patient. The TSs serve as a personalized record of what transpired in the tutorial session. Each student will maintain a private TS and the tutor will maintain a shared TS, viewable by all members of the group. The network communication interface will permit the participants in the tutorial to direct electronic messages to each other. The communication interface has two components: the client software available on the student's and tutor's workstation and the server software. The CMTL client software consists of two applications-one for sending messages and one for viewing the stream of incoming messages. Research is planned to investigate the effects of computer-mediation on the tutorial process.
Lack of familiarity with early signs of autism by community service providers has resulted in significant delays in children receiving early intervention services necessary to improve long-term outcomes. The Screening Tool for Autism in Toddlers and Young Children (STAT) was specifically developed to identify early behavioral features of autism. Although STAT training has been available for years, access is limited because of few STAT trainers and geographic concerns. This study evaluated the efficacy and acceptability of Web-based training of the STAT as a means of increasing accessibility to this training.
Materials and Methods
Thirty professionals from three geographic areas participated. Roughly 1 of 3 had little or no training on autism assessment. The tutorial contains a general overview, administration and scoring conventions, and item-specific content and concepts. Participants completed a pretest and then completed the STAT tutorial at their own pace, followed by a post-test and a user satisfaction questionnaire.
Mean scores on STAT concepts significantly improved after taking the tutorial (p < 0.001). At pretest, only 1 person (3%) obtained correct scores on at least 80% of the items (a priori cutoff for a “pass”), compared with 22 (73%) at post-test (p < 0.001). The majority of trainees enjoyed taking the tutorial, thought it was well organized, relevant, interesting, and useful, and felt it was easy to understand and operate.
Results support Web-based training as a promising method for promoting early identification of autism and may help overcome problems associated with the critical shortage of autism-screening professionals.
autism; diagnosis; training; Internet; computer-assisted instruction
Advances in computing and telecommunications have resulted in the availability of a range of online tools for use in pathology training and quality assurance. The majority focus on either enabling pathologists to examine and diagnose cases, or providing image archives that serve as reference material. Limited emphasis has been placed on analysing the diagnostic process used by pathologists to reach a diagnosis and using this as a resource for improving diagnostic performance.
The ReplaySuite is an online pathology software tool that presents archived virtual slide examinations to pathologists in an accessible video-like format, similar to observing examinations with a double-headed microscope. Delivered through a customised web browser, it utilises PHP (Hypertext PreProcessor) to interact with a remote database and retrieve data describing virtual slide examinations, performed using the Virtual Pathology Slide (VPS).
To demonstrate the technology and conduct a preliminary evaluation of pathologists opinions on its potential application in pathology training and quality assurance, 70 pathologists were invited to use the application to review their own and other pathologists examinations of 10 needle-core breast biopsies and complete an electronic survey. 9 pathologists participated, and all subsequently completed an exit survey.
Of those who replayed an examination by another pathologist, 83.3% (5/6) agreed that replays provided an insight into the examining pathologists diagnosis and 33.3% (2/6) reconsidered their own diagnosis for at least one case. Of those who reconsidered their original diagnosis, all re-classified either concordant with group consensus or original glass slide diagnosis. 77.7% (7/9) of all participants, and all 3 participants who replayed more than 10 examinations stated the ReplaySuite to be of some or great benefit in pathology training and quality assurance.
Participants conclude the ReplaySuite to be of some or of great potential benefit to pathology training and quality assurance and consider the ReplaySuite to be beneficial in evaluating the diagnostic trace of an examination. The ReplaySuite removes temporal and spatial issues that surround the use of double-headed microscopes by allowing examinations to be reviewed at different times and in different locations to the original examination. While the evaluation set was limited and potentially subject to bias, the response of participants was favourable. Further work is planned to determine whether use of the ReplaySuite can result in improved diagnostic ability.
Telepathology; Virtual Slide; Pathology; Education; Quality Assurance; Double-Headed Microscope
The Arrowsmith two-node search is a strategy that is designed to assist biomedical investigators in formulating and assessing scientific hypotheses. More generally, it allows users to identify biologically meaningful links between any two sets of articles A and C in PubMed, even when these share no articles or authors in common and represent disparate topics or disciplines. The key idea is to relate the two sets of articles via title words and phrases (B-terms) that they share. We have created a free, public web-based version of the two-node search tool (http://arrowsmith.psych.uic.edu), have described its development and implementation, and have presented analyses of individual two-node searches. In this paper, we provide an updated tutorial intended for end-users, that covers the use of the tool for a variety of potential scientific use case scenarios. For example, one can assess a recent experimental, clinical or epidemiologic finding that connects two disparate fields of inquiry -- identifying likely mechanisms to explain the finding, and choosing promising follow-up lines of investigation. Alternatively, one can assess whether the existing scientific literature lends indirect support to a hypothesis posed by the user that has not yet been investigated. One can also employ two-node searches to search for novel hypotheses. Arrowsmith provides a service that cannot be carried out feasibly via standard PubMed searches or by other available text mining tools.
text mining; web server; hypothesis; literature-based discovery
The Gibbs Centroid Sampler is a software package designed for locating conserved elements in biopolymer sequences. The Gibbs Centroid Sampler reports a centroid alignment, i.e. an alignment that has the minimum total distance to the set of samples chosen from the a posteriori probability distribution of transcription factor binding-site alignments. In so doing, it garners information from the full ensemble of solutions, rather than only the single most probable point that is the target of many motif-finding algorithms, including its predecessor, the Gibbs Recursive Sampler. Centroid estimators have been shown to yield substantial improvements, in both sensitivity and positive predictive values, to the prediction of RNA secondary structure and motif finding. The Gibbs Centroid Sampler, along with interactive tutorials, an online user manual, and information on downloading the software, is available at: http://bayesweb.wadsworth.org/gibbs/gibbs.html.