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1.  EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management 
BMC Bioinformatics  2008;9:493.
Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management.
EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms.
EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume.
PMCID: PMC2615452  PMID: 19032776
2.  MetNet Online: a novel integrated resource for plant systems biology 
BMC Bioinformatics  2012;13:267.
Plants are important as foods, pharmaceuticals, biorenewable chemicals, fuel resources, bioremediation tools and general tools for recombinant technology. The study of plant biological pathways is advanced by easy access to integrated data sources. Today, various plant data sources are scattered throughout the web, making it increasingly complicated to build comprehensive datasets.
MetNet Online is a web-based portal that provides access to a regulatory and metabolic plant pathway database. The database and portal integrate Arabidopsis, soybean (Glycine max) and grapevine (Vitis vinifera) data. Pathways are enriched with known or predicted information on sub cellular location. MetNet Online enables pathways, interactions and entities to be browsed or searched by multiple categories such as sub cellular compartment, pathway ontology, and GO term. In addition to this, the “My MetNet” feature allows registered users to bookmark content and track, import and export customized lists of entities. Users can also construct custom networks using existing pathways and/or interactions as building blocks.
The site can be reached at Extensive video tutorials on how to use the site are available through
PMCID: PMC3483157  PMID: 23066841
3.  Interactive film scenes for tutor training in problem-based learning (PBL): dealing with difficult situations 
BMC Medical Education  2010;10:52.
In problem-based learning (PBL), tutors play an essential role in facilitating and efficiently structuring tutorials to enable students to construct individual cognitive networks, and have a significant impact on students' performance in subsequent assessments. The necessity of elaborate training to fulfil this complex role is undeniable. In the plethora of data on PBL however, little attention has been paid to tutor training which promotes competence in the moderation of specific difficult situations commonly encountered in PBL tutorials.
Major interactive obstacles arising in PBL tutorials were identified from prior publications. Potential solutions were defined by an expert group. Video clips were produced addressing the tutor's role and providing exemplary solutions. These clips were embedded in a PBL tutor-training course at our medical faculty combining PBL self-experience with a non-medical case. Trainees provided pre- and post-intervention self-efficacy ratings regarding their PBL-related knowledge, skills, and attitudes, as well as their acceptance and the feasibility of integrating the video clips into PBL tutor-training (all items: 100 = completely agree, 0 = don't agree at all).
An interactive online tool for PBL tutor training was developed comprising 18 video clips highlighting difficult situations in PBL tutorials to encourage trainees to develop and formulate their own intervention strategies. In subsequent sequences, potential interventions are presented for the specific scenario, with a concluding discussion which addresses unresolved issues.
The tool was well accepted and considered worth the time spent on it (81.62 ± 16.91; 62.94 ± 16.76). Tutors considered the videos to prepare them well to respond to specific challenges in future tutorials (75.98 ± 19.46). The entire training, which comprised PBL self-experience and video clips as integral elements, improved tutor's self-efficacy with respect to dealing with problematic situations (pre: 36.47 ± 26.25, post: 66.99 ± 21.01; p < .0001) and significantly increased appreciation of PBL as a method (pre: 61.33 ± 24.84, post: 76.20 ± 20.12; p < .0001).
The interactive tool with instructional video clips is designed to broaden the view of future PBL tutors in terms of recognizing specific obstacles to functional group dynamics and developing individual intervention strategies. We show that this tool is well accepted and can be successfully integrated into PBL tutor-training. Free access is provided to the entire tool at
PMCID: PMC2909975  PMID: 20604927
4.  A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis 
PLoS Computational Biology  2014;10(6):e1003670.
A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.
Author Summary
We propose a workflow to map the expression domains of multiple genes onto a series of 3D templates, or “atlas”, during early embryogenesis. It was applied to the zebrafish at different stages between 4 and 6.3 hpf, generating 6 templates. Our system overcomes the lack of significant morphological landmarks in early development by relying on the expression of a reference gene (goosecoid, gsc) and nuclear staining to guide the registration of the analyzed genes. The proposed method also successfully maps gene domains from partially imaged embryos, thus allowing greater microscope magnification and cellular resolution. By using the workflow to construct a spatiotemporal database of zebrafish, we opened the way to a systematic analysis of vertebrate embryogenesis. The atlas database, together with the mapping software (Match-IT), a custom-made visualization platform (Atlas-IT), and step-by-step user guides are available from the Supplementary Material. We expect that this will encourage other laboratories to generate, map, visualize and analyze new gene expression datasets.
PMCID: PMC4063669  PMID: 24945246
5.  A self-updating road map of The Cancer Genome Atlas 
Bioinformatics  2013;29(10):1333-1340.
Motivation: Since 2011, The Cancer Genome Atlas’ (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is instantiated in only partially overlapping sets of analytical platforms, while the number of data files available doubles approximately every 7 months.
Results: We developed an engine to index and annotate the TCGA files, relying exclusively on third-generation web technologies (Web 3.0). Specifically, this engine uses JavaScript in conjunction with the World Wide Web Consortium’s (W3C) Resource Description Framework (RDF), and SPARQL, the query language for RDF, to capture metadata of files in the TCGA open-access HTTP directory. The resulting index may be queried using SPARQL, and enables file-level provenance annotations as well as discovery of arbitrary subsets of files, based on their metadata, using web standard languages. In turn, these abilities enhance the reproducibility and distribution of novel results delivered as elements of a web-based computational ecosystem. The development of the TCGA Roadmap engine was found to provide specific clues about how biomedical big data initiatives should be exposed as public resources for exploratory analysis, data mining and reproducible research. These specific design elements align with the concept of knowledge reengineering and represent a sharp departure from top-down approaches in grid initiatives such as CaBIG. They also present a much more interoperable and reproducible alternative to the still pervasive use of data portals.
Availability: A prepared dashboard, including links to source code and a SPARQL endpoint, is available at A video tutorial is available at
PMCID: PMC3654710  PMID: 23595662
6.  A new approach for visualisation of dye leakage in fluorescein angiography 
Fluorescein angiography (FA) is the more common investigation performed for macular diseases.1 Frozen FA pictures are obtained but direct visualisation of the kinetics of FA is possible only once, by the investigator. The kinetics of FA examination is imagined from static FA pictures based on our experience.23 We evaluated a new software that re‐create automatic pseudo‐movie from static pictures, in order to share the visualisation of dye leakage.
EyeToolkit software (EDC Lamy EyeToolkit software, EDC LAMY, Carvin, France) performs an automatic and rapid overlay (0.5 to 3 seconds) from the different angiographic frames. Five images from the same examination, from early to late phase, are required to generate a movie. The resulting movies could be seen either with the EyeToolkit software or be exported to video format. We submitted a minimum of six images issued from printed photographs or any digital instrument (Topcon retinal camera, TRC‐50, Topcon, Tokyo, Japan; Heidelberg Retina Angiograph, HRA 2, Heidelberg Engineering, Heidelberg, Germany), to the EyeToolkit software: sequences of fluorescein angiograms of patients harbouring various patterns of exudative age‐related macular degeneration (AMD), with or without treatment, were selected in order to visualise active leakage of dye and to differentiate it from staining. In addition, we submitted to the EyeToolkit software images issued from one single FA examination (early phase to 10′) in case of central serous chorioretinopathy (CSC), in order to see the kinetics of the leakage and to visualise leakage of dye from active areas of CSC.
We evaluated two kinds of leakage: chorio‐retinal leakage from choroidal new vessels (CNVs) due to AMD, and retinal leakage from active areas of CSC. In exudative AMD patients, the rapid overlay (<10”) applied in a movie mode obviously demonstrated the progressive enlargement of the hyperfluorescence, materialising the leakage of fluorescein from CNVs. The FA movies generated with EyeToolkit permitted to clearly see the active leakage from a newly diagnosed classic CNV (Video 1), and from a newly diagnosed minimally classic CNV (Video 2). Moreover, the FA movies generated with EyeToolkit permitted to easily detect the minimal leakage from a still active classic choroidal neovascularisation previously treated by photodynamic therapy (PDT) (Video 3), and to visualise the filling of the vascularised pigment epithelium detachment from an occult choroidal neovascularisation previously treated by PDT (Video 4). In CSC, the FA movies generated with EyeToolkit permitted to see the kinetics of the classic smokestack‐type leakage (Video 5) and to easily visualise leakage of dye from active areas of CSC (Video 6). EyeToolkit software is a new automatic and efficient tool for a rapid overlay of images, obtaining an angiographic movie from any image. It leads to easy visualisation of leakage from CNVs and from active areas of CSC; thus, owing to the easy differentiation of active leakage from staining, EyeToolkit software would seem particularly helpful for the decision of treatment and re‐treatment. Easy visibility of the kinetics of the dye in angiography, in a movie mode, also represents a useful approach for teaching. Based on this preliminary analysis, this software can be considered for (1) recreating pseudo‐kinetics of dye in retinal angiography, (2) easy sharing of retinal angiograhy; voice comments can be included within the file, and (3) teaching and e‐learning. The comparative evaluation of the generated movies versus classic angiographic pictures must validate its use for diagnosis and indications of treatment.
See online video reports
To view the full report and accompanying video please go to:
All videos from the BJO video report collection are available from:
PMCID: PMC2095509  PMID: 18024812
7.  A randomized controlled pilot trial comparing the impact of access to clinical endocrinology video demonstrations with access to usual revision resources on medical student performance of clinical endocrinology skills 
BMC Medical Education  2013;13:135.
Demonstrating competence in clinical skills is key to course completion for medical students. Methods of providing clinical instruction that foster immediate learning and potentially serve as longer-term repositories for on-demand revision, such as online videos demonstrating competent performance of clinical skills, are increasingly being used. However, their impact on learning has been little studied. The aim of this study was to determine the value of adjunctive on-demand video-based training for clinical skills acquisition by medical students in endocrinology.
Following an endocrinology clinical tutorial program, 2nd year medical students in the pre-assessment revision period were recruited and randomized to either a set of bespoke on-line clinical skills training videos (TV), or to revision as usual (RAU). The skills demonstrated on video were history taking in diabetes mellitus (DMH), examination for diabetes lower limb complications (LLE), and examination for signs of thyroid disease (TE). Students were assessed on these clinical skills in an observed structured clinical examination two weeks after randomization. Assessors were blinded to student randomization status.
For both diabetes related clinical skills assessment tasks, students in the TV group performed significantly better than those in the RAU group. There were no between group differences in thyroid examination performance. For the LLE, 91.7% (n = 11/12) of students randomized to the video were rated globally as competent at the skill compared with 40% (n = 4/10) of students not randomized to the video (p = 0.024). For the DMH, 83.3% (n = 10/12) of students randomized to the video were rated globally as competent at the skill compared with 20% (n = 2/10) of students not randomized to the video (p = 0.007).
Exposure to high quality videos demonstrating clinical skills can significantly improve medical student skill performance in an observed structured clinical examination of these skills, when used as an adjunct to clinical skills face-to-face tutorials and deliberate practice of skills in a blended learning format. Video demonstrations can provide an enduring, on-demand, portable resource for revision, which can even be used at the bedside by learners. Such resources are cost-effectively scalable for large numbers of learners.
PMCID: PMC3851453  PMID: 24090039
Video; Clinical skills; Medical student; Endocrinology; Medical education; E-learning
8.  Translational biomarker discovery in clinical metabolomics: an introductory tutorial 
Metabolomics  2012;9(2):280-299.
Metabolomics is increasingly being applied towards the identification of biomarkers for disease diagnosis, prognosis and risk prediction. Unfortunately among the many published metabolomic studies focusing on biomarker discovery, there is very little consistency and relatively little rigor in how researchers select, assess or report their candidate biomarkers. In particular, few studies report any measure of sensitivity, specificity, or provide receiver operator characteristic (ROC) curves with associated confidence intervals. Even fewer studies explicitly describe or release the biomarker model used to generate their ROC curves. This is surprising given that for biomarker studies in most other biomedical fields, ROC curve analysis is generally considered the standard method for performance assessment. Because the ultimate goal of biomarker discovery is the translation of those biomarkers to clinical practice, it is clear that the metabolomics community needs to start “speaking the same language” in terms of biomarker analysis and reporting-especially if it wants to see metabolite markers being routinely used in the clinic. In this tutorial, we will first introduce the concept of ROC curves and describe their use in single biomarker analysis for clinical chemistry. This includes the construction of ROC curves, understanding the meaning of area under ROC curves (AUC) and partial AUC, as well as the calculation of confidence intervals. The second part of the tutorial focuses on biomarker analyses within the context of metabolomics. This section describes different statistical and machine learning strategies that can be used to create multi-metabolite biomarker models and explains how these models can be assessed using ROC curves. In the third part of the tutorial we discuss common issues and potential pitfalls associated with different analysis methods and provide readers with a list of nine recommendations for biomarker analysis and reporting. To help readers test, visualize and explore the concepts presented in this tutorial, we also introduce a web-based tool called ROCCET (ROC Curve Explorer & Tester, ROCCET was originally developed as a teaching aid but it can also serve as a training and testing resource to assist metabolomics researchers build biomarker models and conduct a range of common ROC curve analyses for biomarker studies.
Electronic supplementary material
The online version of this article (doi:10.1007/s11306-012-0482-9) contains supplementary material, which is available to authorized users.
PMCID: PMC3608878  PMID: 23543913
Biomarker analysis; ROC curve; AUC; Confidence intervals; Optimal threshold; Sample size; Bootstrapping; Cross validation; Biomarker validation and reporting
9.  Health Professional Learner Attitudes and Use of Digital Learning Resources 
Web-based digital repositories allow educational resources to be accessed efficiently and conveniently from diverse geographic locations, hold a variety of resource formats, enable interactive learning, and facilitate targeted access for the user. Unlike some other learning management systems (LMS), resources can be retrieved through search engines and meta-tagged labels, and content can be streamed, which is particularly useful for multimedia resources.
The aim of this study was to examine usage and user experiences of an online learning repository (Physeek) in a population of physiotherapy students. The secondary aim of this project was to examine how students prefer to access resources and which resources they find most helpful.
The following data were examined using an audit of the repository server: (1) number of online resources accessed per day in 2010, (2) number of each type of resource accessed, (3) number of resources accessed during business hours (9 am to 5 pm) and outside business hours (years 1-4), (4) session length of each log-on (years 1-4), and (5) video quality (bit rate) of each video accessed. An online questionnaire and 3 focus groups assessed student feedback and self-reported experiences of Physeek.
Students preferred the support provided by Physeek to other sources of educational material primarily because of its efficiency. Peak usage commonly occurred at times of increased academic need (ie, examination times). Students perceived online repositories as a potential tool to support lifelong learning and health care delivery.
The results of this study indicate that today’s health professional students welcome the benefits of online learning resources because of their convenience and usability. This represents a transition away from traditional learning styles and toward technological learning support and may indicate a growing link between social immersions in Internet-based connections and learning styles. The true potential for Web-based resources to support student learning is as yet unknown.
PMCID: PMC3636135  PMID: 23324800
Information storage and retrieval; Medical Informatics; Education, professional
10.  Are you ready for an office code blue?  
Canadian Family Physician  2015;61(1):e9-e16.
Problem being addressed
Medical emergencies occur commonly in offices of family physicians, yet many offices are poorly prepared for emergencies. An Internet-based educational video discussing office emergencies might improve the responses of physicians and their staff to emergencies, yet such a tool has not been previously described.
Objective of program
To use evidence-based practices to develop an educational video detailing preparation for emergencies in medical offices, disseminate the video online, and evaluate the attitudes of physicians and their staff toward the video.
Program description
A 6-minute video was created using a review of recent literature and Canadian regulatory body policies. The video describes recommended emergency equipment, emergency response improvement, and office staff training. Physicians and their staff were invited to view the video online at Viewers’ opinions of the video format and content were assessed by survey (n = 275).
Survey findings indicated the video was well presented and relevant, and the Web-based format was considered convenient and satisfactory. Participants would take other courses using this technology, and agreed this program would enhance patient care.
PMCID: PMC4301781  PMID: 25609541
11.  Nervous system examination on YouTube 
BMC Medical Education  2012;12:126.
Web 2.0 sites such as YouTube have become a useful resource for knowledge and are used by medical students as a learning resource. This study aimed at assessing videos covering the nervous system examination on YouTube.
A research of YouTube was conducted from 2 November to 2 December 2011 using the following key words “nervous system examination”, “nervous system clinical examination”, “cranial nerves examination”, “CNS examination”, “examination of cerebellum”, “balance and coordination examination”. Only relevant videos in the English language were identified and related URL recorded. For each video, the following information was collected: title, author/s, duration, number of viewers, number of posted comments, and total number of days on YouTube. Using criteria comprising content, technical authority and pedagogy parameters, videos were rated independently by three assessors and grouped into educationally useful and non-educationally useful.
A total of 2240 videos were screened; 129 were found to have relevant information to nervous system examination. Analysis revealed that 61 (47%) of the videos provided useful information on the nervous system examination. These videos scored (mean ± SD, 14.9 ± 0.2) and mainly covered examination of the whole nervous system (8 videos, 13%), cranial nerves (42 videos, 69%), upper limbs (6 videos, 10%), lower limbs (3 videos, 5%), balance and co-ordination (2 videos, 3%). The other 68 (53%) videos were not useful educationally; scoring (mean ± SD, 11.1 ± 3.0). The total viewers of all videos was 2,189,434. Useful videos were viewed by 1,050,445 viewers (48% of total viewers). The total viewership per day for useful videos was 1,794.5 and for non-useful videos 1,132.0. The differences between the three assessors were insignificant (less than 0.5 for the mean and 0.3 for the SD).
Currently, YouTube provides an adequate resource for learning nervous system examination, which can be used by medical students. However, there were deficiencies in videos covering examination of the cerebellum and balance system. Useful videos can be used as learning resources to medical students.
PMCID: PMC3548753  PMID: 23259768
YouTube; Medical education; Nervous system examination; Web-2; Learning resources
12.  TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model 
Nucleic Acids Research  2014;42(Web Server issue):W442-W448.
TogoTable ( is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output.
PMCID: PMC4086138  PMID: 24829452
13.  TogoDoc Server/Client System: Smart Recommendation and Efficient Management of Life Science Literature 
PLoS ONE  2010;5(12):e15305.
In this paper, we describe a server/client literature management system specialized for the life science domain, the TogoDoc system (Togo, pronounced Toe-Go, is a romanization of a Japanese word for integration). The server and the client program cooperate closely over the Internet to provide life scientists with an effective literature recommendation service and efficient literature management. The content-based and personalized literature recommendation helps researchers to isolate interesting papers from the “tsunami” of literature, in which, on average, more than one biomedical paper is added to MEDLINE every minute. Because researchers these days need to cover updates of much wider topics to generate hypotheses using massive datasets obtained from public databases or omics experiments, the importance of having an effective literature recommendation service is rising. The automatic recommendation is based on the content of personal literature libraries of electronic PDF papers. The client program automatically analyzes these files, which are sometimes deeply buried in storage disks of researchers' personal computers. Just saving PDF papers to the designated folders makes the client program automatically analyze and retrieve metadata, rename file names, synchronize the data to the server, and receive the recommendation lists of newly published papers, thus accomplishing effortless literature management. In addition, the tag suggestion and associative search functions are provided for easy classification of and access to past papers (researchers who read many papers sometimes only vaguely remember or completely forget what they read in the past). The TogoDoc system is available for both Windows and Mac OS X and is free. The TogoDoc Client software is available at, and the TogoDoc server is available at
PMCID: PMC3001491  PMID: 21179453
14.  The Rat Genome Database 2009: variation, ontologies and pathways 
Nucleic Acids Research  2008;37(Database issue):D744-D749.
The Rat Genome Database (RGD, was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through to the level of the whole organism, including the variations associated with disease phenotypes. To fully support use of the rat as a translational model for biological systems and human disease, RGD continues to curate these datasets while enhancing and developing tools to allow efficient and effective access to the data in a variety of formats including linear genome viewers, pathway diagrams and biological ontologies. To support pathophysiological analysis of data, RGD Disease Portals provide an entryway to integrated gene, QTL and strain data specific to a particular disease. In addition to tool and content development and maintenance, RGD promotes rat research and provides user education by creating and disseminating tutorials on the curated datasets, submission processes, and tools available at RGD. By curating, storing, integrating, visualizing and promoting rat data, RGD ensures that the investment made into rat genomics and genetics can be leveraged by all interested investigators.
PMCID: PMC2686558  PMID: 18996890
15.  e-MIR2: a public online inventory of medical informatics resources 
Over the past years, the number of available informatics resources in medicine has grown exponentially. While specific inventories of such resources have already begun to be developed for Bioinformatics (BI), comparable inventories are as yet not available for the Medical Informatics (MI) field, so that locating and accessing them currently remains a difficult and time-consuming task.
We have created a repository of MI resources from the scientific literature, providing free access to its contents through a web-based service. We define informatics resources as all those elements that constitute, serve to define or are used by informatics systems, ranging from architectures or development methodologies to terminologies, vocabularies, databases or tools. Relevant information describing the resources is automatically extracted from manuscripts published in top-ranked MI journals. We used a pattern matching approach to detect the resources’ names and their main features. Detected resources are classified according to three different criteria: functionality, resource type and domain. To facilitate these tasks, we have built three different classification schemas by following a novel approach based on folksonomies and social tagging. We adopted the terminology most frequently used by MI researchers in their publications to create the concepts and hierarchical relationships belonging to the classification schemas. The classification algorithm identifies the categories associated with resources and annotates them accordingly. The database is then populated with this data after manual curation and validation.
We have created an online repository of MI resources to assist researchers in locating and accessing the most suitable resources to perform specific tasks. The database contains 609 resources at the time of writing and is available at We are continuing to expand the number of available resources by taking into account further publications as well as suggestions from users and resource developers.
PMCID: PMC3441434  PMID: 22857741
Medical informatics; Cataloging; Classification; Software resources; Information storage and retrieval; Search engine; Database; Information management; Folksonomies; Social tagging
16.  Effectiveness of YouTube as a Source of Medical Information on Heart Transplantation 
In this digital era, there is a growing tendency to use the popular Internet site YouTube as a new electronic-learning (e-learning) means for continuing medical education. Heart transplantation (HTx) remains the most viable option for patients with end-stage heart failure or severe coronary artery disease. There are plenty of freely accessible YouTube videos providing medical information about HTx.
The aim of the present study is to determine the effectiveness of YouTube as an e-learning source on HTx.
In order to carry out this study, YouTube was searched for videos uploaded containing surgical-related information using the four keywords: (1) “heart transplantation”, (2) “cardiac transplantation”, (3) “heart transplantation operation”, and (4) “cardiac transplantation operation”. Only videos in English (with comments or subtitles in English language) were included. Two experienced cardiac surgeons watched each video (N=1800) and classified them as useful, misleading, or recipients videos based on the HTx-relevant information. The kappa statistic was used to measure interobserver variability. Data was analyzed according to six types of YouTube characteristics including “total viewership”, “duration”, “source”, “days since upload”, “scores” given by the viewers, and specialized information contents of the videos.
A total of 342/1800 (19.00%) videos had relevant information about HTx. Of these 342 videos, 215 (62.8%) videos had useful information about specialized knowledge, 7/342 (2.0%) were found to be misleading, and 120/342 (35.1%) only concerned recipients’ individual issues. Useful videos had 56.09% of total viewership share (2,175,845/3,878,890), whereas misleading had 35.47% (1,375,673/3,878,890). Independent user channel videos accounted for a smaller proportion (19% in total numbers) but might have a wider impact on Web viewers, with the highest mean views/day (mean 39, SD 107) among four kinds of channels to distribute HTx-related information.
YouTube videos on HTx benefit medical professionals by providing a substantial amount of information. However, it is a time-consuming course to find high-quality videos. More authoritative videos by trusted sources should be posted for dissemination of reliable information. With an improvement of ranking system and content providers in future, YouTube, as a freely accessible outlet, will help to meet the huge informational needs of medical staffs and promote medical education on HTx.
PMCID: PMC3841345  PMID: 24263225
heart transplantation; Internet; medical informatics; online videos; YouTube; e-learning
17.  Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education 
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.
PMCID: PMC1564136  PMID: 16911779
18.  INDIAM—An e-Learning System for the Interpretation of Mammograms 
We propose the design of a teaching system named Interpretation and Diagnosis of Mammograms (INDIAM) for training students in the interpretation of mammograms and diagnosis of breast cancer. The proposed system integrates an illustrated tutorial on radiology of the breast, that is, mammography, which uses education techniques to guide the user (doctors, students, or researchers) through various concepts related to the diagnosis of breast cancer. The user can obtain informative text about specific subjects, access a library of bibliographic references, and retrieve cases from a mammographic database that are similar to a query case on hand. The information of each case stored in the mammographic database includes the radiological findings, the clinical history, the lifestyle of the patient, and complementary exams. The breast cancer tutorial is linked to a module that simulates the analysis and diagnosis of a mammogram. The tutorial incorporates tools for helping the user to evaluate his or her knowledge about a specific subject by using the education system or by simulating a diagnosis with appropriate feedback in case of error. The system also makes available digital image processing tools that allow the user to draw the contour of a lesion, the contour of the breast, or identify a cluster of calcifications in a given mammogram. The contours provided by the user are submitted to the system for evaluation. The teaching system is integrated with AMDI—An Indexed Atlas of Digital Mammograms—that includes case studies, e-learning, and research systems. All the resources are accessible via the Web.
PMCID: PMC3043705  PMID: 18425550
Education; medical; computer-assisted instruction; computers in medicine; digital mammography
19.  Bandwidth Constraints to Using Video and Other Rich Media in Behavior Change Websites 
Web-based behavior change interventions often include rich media (eg, video, audio, and large graphics). The rationale for using rich media includes the need to reach users who are not inclined or able to use text-based website content, encouragement of program engagement, and following the precedent set by news and sports websites.
We describe the development of a bandwidth usage index, which seeks to provide a practical method to gauge the extent to which websites can successfully be used within different Internet access scenarios (eg, dial-up and broadband).
We conducted three studies to measure bandwidth consumption. In Study 1, we measured the bandwidth usage index for three video-rich websites (for smoking cessation, for caregivers, and for improving eldercare by family members). We then estimated the number of concurrent users that could be accommodated by each website under various Internet access scenarios. In Study 2, we sought to validate our estimated threshold number of concurrent users by testing the video-rich smoking cessation website with different numbers of concurrent users. In Study 3, we calculated the bandwidth usage index and threshold number of concurrent users for three versions of the smoking cessation website: the video-rich version (tested in Study 1), an audio-rich version, and a Web-enabled CD-ROM version in which all media-rich content was placed on a CD-ROM on the client computer.
In Study 1, we found that the bandwidth usage index of the video-rich websites ranged from 144 Kbps to 93 Kbps. These results indicated that dial-up modem users would not achieve a “good user experience” with any of the three rich media websites. Results for Study 2 confirmed that usability was compromised when the estimated threshold number of concurrent users was exceeded. Results for Study 3 indicated that changing a website from video- to audio-rich content reduced the bandwidth requirement by almost 50%, but it remained too large to allow satisfactory use in dial-up modem scenarios. The Web-enabled CD-ROM reduced bandwidth requirements such that even a dial-up modem user could have a good user experience with the rich media content.
We conclude that the bandwidth usage index represents a practical tool that can help developers and researchers to measure the bandwidth requirements of their websites as well as to evaluate the feasibility of certain website designs in terms of specific use cases. These findings are discussed in terms of reaching different groups of users as well accommodating the intended number of concurrent users. We also discuss the promising option of using Web-enabled CD-ROMs to deliver rich media content to users with dial-up Internet access. We introduce a number of researchable themes for improving our ability to develop Web-based behavior change interventions that can better deliver what they promise.
PMCID: PMC1550668  PMID: 16236701
Health behavior; Internet; behavioral research; rich media; video; smoking cessation; bandwidth usage index
20.  The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video 
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:
PMCID: PMC3096322  PMID: 21565781
21.  A Self-Study Tutorial using the Allen Brain Explorer and Brain Atlas to Teach Concepts of Mammalian Neuroanatomy and Brain Function 
The Allen Brain Atlas is a repository of neuroanatomical data concerning the mouse brain. The core of the database is a Nissl-stained reference atlas of the brain accompanied by in situ hybridization data for essentially the entire mouse genome. This database is freely available at the Allen Institute for Brain Science website, as is an innovative tool to explore the database, the Brain Explorer. This tool is downloaded and installed on your own computer. I have developed a self-study tutorial, “Explorations with the Allen Brain Explorer”, which uses the Brain Explorer and the Brain Atlas to teach fundamentals of mammalian neuroanatomy and brain function. In this tutorial background information and step-by-step exercises on the use of the Brain Explorer are given using PowerPoint as a platform. To do the tutorial both the PowerPoint and the Brain Explorer are opened on the computer and the students switch from one program to the other as they go, in a step-wise fashion, through the various exercises. There are two main groups of exercises, titled “The Basics” and “Explorations”, with both groups accessed from a PowerPoint “Start Menu” by clicking on dynamic links to the appropriate exercises. Most exercises have a number of dynamic links to PowerPoint slides where background information for the exercises is given or the neuroanatomical data collected from the Brain Atlas is discussed.
PMCID: PMC3592706  PMID: 23493964
Allen Brain Atlas; Brain Explorer; mouse brain neuroanatomy; olfactory system; limbic system; hypothalamus; hippocampus; reward center; in situ hybridization; gene expression
22.  Experience with multimodality telepathology at the University of Pittsburgh Medical Center 
Several modes of telepathology exist including static (store-and-forward), dynamic (live video streaming or robotic microscopy), and hybrid technology involving whole slide imaging (WSI). Telepathology has been employed at the University of Pittsburgh Medical Center (UPMC) for over a decade at local, national, and international sites. All modes of telepathology have been successfully utilized to exploit our institutions subspecialty expertise and to compete for pathology services. This article discusses the experience garnered at UPMC with each of these teleconsultation methods. Static and WSI telepathology systems have been utilized for many years in transplant pathology using a private network and client-server architecture. Only minor clinically significant differences of opinion were documented. In hematopathology, the CellaVision® system is used to transmit, via email, static images of blood cells in peripheral blood smears for remote interpretation. While live video streaming has remained the mode of choice for providing immediate adequacy assessment of cytology specimens by telecytology, other methods such as robotic microscopy have been validated and shown to be effective. Robotic telepathology has been extensively used to remotely interpret intra-operative neuropathology consultations (frozen sections). Adoption of newer technology and increased pathologist experience has improved accuracy and deferral rates in teleneuropathology. A digital pathology consultation portal ( was recently created at our institution to facilitate digital pathology second opinion consults, especially for WSI. The success of this web-based tool is the ability to handle vendor agnostic, large image files of digitized slides, and ongoing user-friendly customization for clients and teleconsultants. It is evident that the practice of telepathology at our institution has evolved in concert with advances in technology and user experience. Early and continued adoption of telepathology has promoted additional digital pathology resources that are now being leveraged for other clinical, educational, and research purposes.
PMCID: PMC3551511  PMID: 23372986
Digital imaging; robotic; static; teleconsultation; telemicroscopy; telepathology; video microscopy; whole slide imaging
23.  SynTView — an interactive multi-view genome browser for next-generation comparative microorganism genomics 
BMC Bioinformatics  2013;14:277.
Dynamic visualisation interfaces are required to explore the multiple microbial genome data now available, especially those obtained by high-throughput sequencing — a.k.a. “Next-Generation Sequencing” (NGS) — technologies; they would also be useful for “standard” annotated genomes whose chromosome organizations may be compared. Although various software systems are available, few offer an optimal combination of feature-rich capabilities, non-static user interfaces and multi-genome data handling.
We developed SynTView, a comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects (annotations). The software is characterised by the presentation of syntenic organisations of microbial genomes and the visualisation of polymorphism data (typically Single Nucleotide Polymorphisms — SNPs) along these genomes; these features are accessible to the user in an integrated way. A variety of specialised views are available and are all dynamically inter-connected (including linear and circular multi-genome representations, dot plots, phylogenetic profiles, SNP density maps, and more). SynTView is not linked to any particular database, allowing the user to plug his own data into the system seamlessly, and use external web services for added functionalities. SynTView has now been used in several genome sequencing projects to help biologists make sense out of huge data sets.
The most important assets of SynTView are: (i) the interactivity due to the Flash technology; (ii) the capabilities for dynamic interaction between many specialised views; and (iii) the flexibility allowing various user data sets to be integrated. It can thus be used to investigate massive amounts of information efficiently at the chromosome level. This innovative approach to data exploration could not be achieved with most existing genome browsers, which are more static and/or do not offer multiple views of multiple genomes. Documentation, tutorials and demonstration sites are available at the URL:
PMCID: PMC3849071  PMID: 24053737
Genome browser; Microbial genomics; Synteny; Next-Generation Sequencing (NGS); Single Nucleotide Polymorphism (SNP); Flash; Interactive graphical user interface
24.  Representation and Misrepresentation of Scientific Evidence in Contemporary Tobacco Regulation: A Review of Tobacco Industry Submissions to the UK Government Consultation on Standardised Packaging 
PLoS Medicine  2014;11(3):e1001629.
Selda Ulucanlar and colleagues analyze submissions by two tobacco companies to the UK government consultation on standardized packaging.
Please see later in the article for the Editors' Summary
Standardised packaging (SP) of tobacco products is an innovative tobacco control measure opposed by transnational tobacco companies (TTCs) whose responses to the UK government's public consultation on SP argued that evidence was inadequate to support implementing the measure. The government's initial decision, announced 11 months after the consultation closed, was to wait for ‘more evidence’, but four months later a second ‘independent review’ was launched. In view of the centrality of evidence to debates over SP and TTCs' history of denying harms and manufacturing uncertainty about scientific evidence, we analysed their submissions to examine how they used evidence to oppose SP.
Methods and Findings
We purposively selected and analysed two TTC submissions using a verification-oriented cross-documentary method to ascertain how published studies were used and interpretive analysis with a constructivist grounded theory approach to examine the conceptual significance of TTC critiques. The companies' overall argument was that the SP evidence base was seriously flawed and did not warrant the introduction of SP. However, this argument was underpinned by three complementary techniques that misrepresented the evidence base. First, published studies were repeatedly misquoted, distorting the main messages. Second, ‘mimicked scientific critique’ was used to undermine evidence; this form of critique insisted on methodological perfection, rejected methodological pluralism, adopted a litigation (not scientific) model, and was not rigorous. Third, TTCs engaged in ‘evidential landscaping’, promoting a parallel evidence base to deflect attention from SP and excluding company-held evidence relevant to SP. The study's sample was limited to sub-sections of two out of four submissions, but leaked industry documents suggest at least one other company used a similar approach.
The TTCs' claim that SP will not lead to public health benefits is largely without foundation. The tools of Better Regulation, particularly stakeholder consultation, provide an opportunity for highly resourced corporations to slow, weaken, or prevent public health policies.
Please see later in the article for the Editors' Summary
Editors' Summary
Every year, about 6 million people die from tobacco-related diseases and, if current trends continue, annual tobacco-related deaths will increase to more than 8 million by 2030. To reduce this loss of life, national and international bodies have drawn up various conventions and directives designed to implement tobacco control measures such as the adoption of taxation policies aimed at reducing tobacco consumption and bans on tobacco advertising, promotion, and sponsorship. One innovative but largely unused tobacco control measure is standardised packaging of tobacco products. Standardised packaging aims to prevent the use of packaging as a marketing tool by removing all brand imagery and text (other than name) and by introducing packs of a standard shape and colour that include prominent pictorial health warnings. Standardised packaging was first suggested as a tobacco control measure in 1986 but has been consistently opposed by the tobacco industry.
Why Was This Study Done?
The UK is currently considering standardised packaging of tobacco products. In the UK, Better Regulation guidance obliges officials to seek the views of stakeholders, including corporations, on the government's cost and benefit estimates of regulatory measures such as standardised packaging and on the evidence underlying these estimates. In response to a public consultation about standardised packaging in July 2013, which considered submissions from several transnational tobacco companies (TTCs), the UK government announced that it would wait for the results of the standardised packaging legislation that Australia adopted in December 2012 before making its final decision about this tobacco control measure. Parliamentary debates and media statements have suggested that doubt over the adequacy of the evidence was the main reason for this ‘wait and see’ decision. Notably, TTCs have a history of manufacturing uncertainty about the scientific evidence related to the harms of tobacco. Given the centrality of evidence to the debate about standardised packaging, in this study, the researchers analyse submissions made by two TTCs, British American Tobacco (BAT) and Japan Tobacco International (JTI), to the first UK consultation on standardised packaging (a second review is currently underway and will report shortly) to examine how TTCs used evidence to oppose standardised packaging.
What Did the Researchers Do and Find?
The researchers analysed sub-sections of two of the four TTC submissions (those submitted by BAT and JTI) made to the public consultation using verification-oriented cross-documentary analysis, which compared references made to published sources with the original sources to ascertain how these sources had been used, and interpretative analysis to examine the conceptual significance of TTC critiques of the evidence on standardised packaging. The researchers report that the companies' overall argument was that the evidence base in support of standardised packaging was seriously flawed and did not warrant the introduction of such packaging. The researchers identified three ways in which the TTC reports misrepresented the evidence base. First, the TTCs misquoted published studies, thereby distorting the main messages of these studies. For example, the TTCs sometimes omitted important qualifying information when quoting from published studies. Second, the TTCs undermined evidence by employing experts to review published studies for methodological rigor and value in ways that did not conform to normal scientific critique approaches (‘mimicked scientific critique’). So, for example, the experts considered each piece of evidence in isolation for its ability to support standardised packaging rather than considering the cumulative weight of the evidence. Finally, the TTCs engaged in ‘evidential landscaping’. That is, they promoted research that deflected attention from standardised packaging (for example, research into social explanations of smoking behaviour) and omitted internal industry research on the role of packaging in marketing.
What Do These Findings Mean?
These findings suggest that the TTC critique of the evidence in favour of standardised packaging that was presented to the UK public consultation on this tobacco control measure is highly misleading. However, because the researchers' analysis only considered subsections of the submissions from two TTCs, these findings may not be applicable to the other submissions or to other TTCs. Moreover, their analysis only considered the efforts made by TTCs to influence public health policy and not the effectiveness of these efforts. Nevertheless, these findings suggest that the claim of TTCs that standardised packaging will not lead to public health benefits is largely without foundation. More generally, these findings highlight the possibility that the tools of Better Regulation, particularly stakeholder consultation, provide an opportunity for wealthy corporations to slow, weaken, or prevent the implementation of public health policies.
Additional Information
Please access these websites via the online version of this summary at
The World Health Organization provides information about the dangers of tobacco (in several languages) and an article about first experiences with Australia's tobacco plain packaging law; for information about the tobacco industry's influence on policy, see the 2009 World Health Organization report ‘Tobacco industry interference with tobacco control’
A UK parliamentary briefing on standardised packaging of tobacco products, a press release about the consultation, and a summary report of the consultation are available; the ideas behind the UK's Better Regulation guidance are described in a leaflet produced by the Better Regulation Task Force
Cancer Research UK (CRUK) has a web page with information on standardised packaging and includes videos
Wikipedia has a page on standardised packaging of tobacco products (note: Wikipedia is a free online encyclopaedia that anyone can edit; available in several languages)
The UK Centre for Tobacco Control Studies is a network of UK universities that undertakes original research, policy development, advocacy, and teaching and training in the field of tobacco control, an online resource managed by the University of Bath, provides up-to-date information on the tobacco industry and the tactics it uses to influence tobacco regulation
SmokeFree, a website provided by the UK National Health Service, offers advice on quitting smoking and includes personal stories from people who have stopped smoking, from the US National Cancer Institute, offers online tools and resources to help people quit smoking
PMCID: PMC3965396  PMID: 24667150
25.  Beyond the electronic textbook model: Software techniques to make on-line educational content dynamic 
Journal of Digital Imaging  2001;14(Suppl 1):108-112.
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.
PMCID: PMC3452717  PMID: 11442066

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