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1.  A Virtual Notebook for biomedical work groups. 
During the past several years, Baylor College of Medicine has made a substantial commitment to the use of information technology in support of its corporate and academic programs. The concept of an Integrated Academic Information Management System (IAIMS) has proved central in our planning, and the IAIMS activities that we have undertaken with funding from the National Library of Medicine have proved to be important extensions of our technology development. Here we describe our Virtual Notebook system, a conceptual and technologic framework for task coordination and information management in biomedical work groups. When fully developed and deployed, the Virtual Notebook will improve the functioning of basic and clinical research groups in the college, and it currently serves as a model for the longer-term development of our entire information management environment.
PMCID: PMC227118  PMID: 3046694
2.  The MEDLINE Retriever. 
Baylor College of Medicine has developed the MEDLINE Retriever, a tool to query MEDLINE, the data-base of medical literature at the National Library of Medicine. The MEDLINE Retriever communicates via the Internet to achieve excellent response time for MEDLINE queries. It uses the X Window System and the Motif toolkit, and employs the Knowbot Operating Environment developed by the Corporation for National Research Initiatives. We discuss the architecture of the MEDLINE Retriever, focusing on the graphical user interface that we have developed, as well as our experiences in developing and deploying the MEDLINE Retriever at Baylor. The MEDLINE Retriever is an extension of Baylor's IAIMS design concept that brought forth the Virtual Notebook System, and fits well with Baylor's aims with regard to the High Performance Computing Initiative.
PMCID: PMC2248138  PMID: 1482920
3.  The ALARM Monitor and the Bone-Marrow Transplant Therapy Advisor: A Demonstration of Two Probabilistic Expert Systems in KNET 
ALARM (A Logical Alarm Reduction Mechanism) is a diagnostic application used to explore probabilistic reasoning techniques in belief networks. ALARM implements an alarm message system for patient monitoring; it calculates probabilities for a differential diagnosis based on available evidence [1]. The medical knowledge is encoded in a graphical structure connecting 8 diagnoses, 16 findings and 13 intermediate variables.
The goal of the ALARM monitoring system is to provide specific text messages advising the user of possible problems. This is a diagnostic task, and we have chosen to represent the relevant knowledge in the language of a belief network. This graphical representation [6] facilitates the integration of qualitative and quantitative knowledge, the assessment of multiple faults, as required by our domain, and nonmonotonic and bidirectional reasoning.
We have also created a belief network, the Bone-Marrow Transplant Therapy Advisor, that represents prognostic factors and their effects on possible outcomes of a bone-marrow transplant. For pediatric patients in the advanced stages of acute lymphoblastic leukemia (ALL), bone-marrow transplantation is generally considered the most promising therapy. For the patient and parents, the decision to proceed with transplantation is often difficult. Morbidity after transplantation is usually severe, and a significant percentage of those who receive a bone marrow transplantation die within a year of transplantation [7]. Many factors, however, offer significant insight into the expected outcome of marrow transplantation. A few examples of such prognostic factors include the white blood count at diagnosis, the age at diagnosis, the number of recurrence episodes before transplantation, and the quality of the match with the marrow donor. Some of those factors indicate the progress of the disease, whereas others define sensitivity to the chemotherapeutic conditioning regimee or the likelihood of Graft-versus-Host Disease (GvHD).
Within the discipline of medical informatics, many researchers have studied methodologies for encoding the knowledge of expert clinicians as computational artifacts. KNET, the support software for ALARM and the bone-marrow transplant advisor, is a general-purpose environment for constructing probabilistic, knowledge-intensive systems based on belief networks and decision networks [2]. KNET differs from other tools for expert-system construction in that it combines a direct-manipulation visual interface with a normative, probabilistic scheme for the management of uncertain information and inference. The KNET architecture defines a complete separation between the hypermedia user interface on the one hand, and the representation and management of expert opinion on the other.
In our laboratory, we and others have used KNET to build not only the ALARM and bone-marrow transplant systems, but also consultation programs for lymph-node pathology and clinical epidemiology [2,4]. KNET imposes few restrictions on the interface design. Indeed, we have rapidly prototyped several direct-manipulation interfaces that use graphics, buttons, menus, text, and icons to organize the display of static and inferred knowledge. The underlying normative representation of knowledge remains constant.
We present ALARM and the transplant therapy advisor as part of a suite of probabilistic, knowledge-intensive medical expert systems. Such systems
• Manage large quantities of extensively cross-referenced information
• Emphasize clarity in acquiring, storing, and displaying expert knowledge
• Incorporate tools for building hypertext user interfaces
• Impose a limited number of constraints on the knowledge engineer's design choices
• Share an axiomatic grounding for diagnosis and decision-making in probability theory and utility theory
• Make normatively correct decisions and diagnoses in the face of uncertain, incomplete, and contradictory information
• Draw inferences from knowledge bases large enough to model significant, real-world medical domains, and do so in polynomial time on low-cost hardware
In this demonstration, we show how ALARM and the therapy advisor synthesize physiologic measurements and prognostic indicators into a diagnostic conclusion according to a belief-network model of the domains. We demonstrate KNET's hypertext interface and the transparent integration of probabilistic reasoning into a diagnostic application. KNET runs on any Macintosh II personal computer with at least 4 megabytes of random-access memory. The authors will provide all the necessary software on a SCSI hard disk. KNET fully supports color and monochrome monitors of any size, and requires no special hardware. We prefer, but do not require, a large color monitor, which demonstrates the capabilities of KNET to greatest advantage.
PMCID: PMC2245721
4.  IAIMS development at Baylor College of Medicine. 
At Baylor College of Medicine, we are developing the technical and intellectual resources needed to realize the Integrated Academic Information Management System (IAIMS) concept fully. The substantial technical, organizational, and financial commitments involved demand that we align our efforts with the strategic purposes of the college. The support of science, therefore, has become the principal, but not exclusive, focus of Baylor's IAIMS effort. Even so, the information technology architecture we have created for biomedical research is proving valuable in other settings as well. And the infrastructure we are creating--the communications architecture and the linkages to information resources--serves many purposes in addition to those of research. The architecture accommodates a diversity of workstations, networks, and informational and computational servers. This will be the greatest possible chance of transferring the fruits of our Phase III development to other academic medical centers.
PMCID: PMC225664  PMID: 1326367
5.  LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory 
PLoS ONE  2013;8(7):e67460.
The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.
Methodology/Principal Findings
We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.
LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.
PMCID: PMC3720848  PMID: 23935832
6.  iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis 
BMC Bioinformatics  2009;10:390.
In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques.
We have developed iLAP (Laboratory data management, Analysis, and Protocol development), a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH) protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from
iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community.
PMCID: PMC2789074  PMID: 19941647
7.  Intelligent Navigation in A Hypertext Mycotoxin Reference Book 
The field of medicine requires a rich and diverse use of technical information. Computer based methods of information access have become common. The use of traditional hierarchical and linear software systems are not efficient enough for the flexible access of information. The network structure of hypertext documents allow for a natural representation of information. Our work concentrates on the issue of navigation in a hypertext information space. The complexity and quantity of medical knowledge means that a user may easily become disoriented when browsing through its hypertext implementation. The weakly structured (non hierarchical) nature of hypertext allows users freedom to explore but such an organization can result in the users becoming lost in the space they are exploring.
SINS (semi-structured intelligent navigation system) is a hypertext environment developed under Hypercard which contains a Toxicology reference manual. SINS's contribution is that it allows intelligent navigation around the toxicology information space. The search for “interesting” information is performed using a “ripple search” mechanism based on the semantic links in the network.
PMCID: PMC2245641
8.  Development of a Google-Based Search Engine for Data Mining Radiology Reports 
The aim of this study is to develop a secure, Google-based data-mining tool for radiology reports using free and open source technologies and to explore its use within an academic radiology department. A Health Insurance Portability and Accountability Act (HIPAA)-compliant data repository, search engine and user interface were created to facilitate treatment, operations, and reviews preparatory to research. The Institutional Review Board waived review of the project, and informed consent was not required. Comprising 7.9 GB of disk space, 2.9 million text reports were downloaded from our radiology information system to a fileserver. Extensible markup language (XML) representations of the reports were indexed using Google Desktop Enterprise search engine software. A hypertext markup language (HTML) form allowed users to submit queries to Google Desktop, and Google’s XML response was interpreted by a practical extraction and report language (PERL) script, presenting ranked results in a web browser window. The query, reason for search, results, and documents visited were logged to maintain HIPAA compliance. Indexing averaged approximately 25,000 reports per hour. Keyword search of a common term like “pneumothorax” yielded the first ten most relevant results of 705,550 total results in 1.36 s. Keyword search of a rare term like “hemangioendothelioma” yielded the first ten most relevant results of 167 total results in 0.23 s; retrieval of all 167 results took 0.26 s. Data mining tools for radiology reports will improve the productivity of academic radiologists in clinical, educational, research, and administrative tasks. By leveraging existing knowledge of Google’s interface, radiologists can quickly perform useful searches.
PMCID: PMC3043709  PMID: 18392657
Google; data mining; reports; HIPAA; search engine
9.  The Global Health Network and globalization of higher education 
The year 2001 and the next millennium will soon be upon us. The major gains in health in the 20th century were primarily the result of improvements in public health including sanitation and immunization. Global health improvements will occur in the 21st century through improvements in information (in particular health training). We will describe a new paradigm for transnational training, the supercourse. In the next century global lecture-shareware training will take place, with Deming based quality control systems on the Internet. Faculty will thus share their best, most passionate lectures on the internet.
During the past 100 years there has been a 25-year increase in life expectancy. It has been estimated that 24 of the 25 years were the result of prevention. Most prevention activity is sharing of information. We are working with leaders from WHO, the World Bank, IBM, NASA, PAHO to create a discipline called telepreventive medicine. This is the application of low band with information systems (the Internet) to large numbers of well people to prevent disease. One of the most important aspect of this work is the establishment globalisation of prevention education; the Supercourse.
Question: What is the best way to improve health training/research?
Answer: Improve the lectures.
Question: How do we improve health training/research lectures:
Answer: Have academic faculty worldwide share their lectures:
Question: Will faculty share lectures?
Answer: Yes, The Supercourse has 1107 faculty from 101 countries who created a Library of Lectures with 110 lectures on the Internet with quality control, and cutting edge cognitive design. This is being shared worldwide.
We are developing a "Library of Lectures" with passionate lectures in public health from across the world such as seen here from South Africa. We propose to expand this to all areas of research in health. Our program consists of:
Shareware: A Global faculty is developing and sharing their best, most passionate lectures. This benefits all. The experienced faculty member can beef up their lectures that are not cutting edge. New instructors reduce preparation time and improve their lectures, as they can employ state of the art lectures from others. Faculty in developing countries have access to current public health information for the first time. The concept is that of a library of lectures for all to use is in many ways similar to that of "shareware" on the computer.
Statistical Quality Assurance: We have established a Deming Model of statistical quality control to monitor lectures over time
Supporting the teachers: The Library of Lectures consists of exciting lectures by public health experts in the field. The classroom teacher "takes" them out for free like a library book. There is no direct teaching of students from a distance, rather the concept of the system is to provide cutting edge material for all faculty to present.
Hypertext comic book: The lectures are icon driven, and the students can go deep into the Internet for more information through hyperlinks. It is based upon PowerPoint for ease of usage
Presentation Speed: We have discovered technologies to speed access to lectures world wide
Text books: The British Medical Association has put 2 current text books on line for us
Multilingual: For global use, this must be multilingual, the first lecture is in 8 languages
Voice-Sound Video: We are using state of the art Internet voice-video systems. We soon will be using "clickable" voice video
We have published over 68 papers in leading medical journals including the Lancet, British Medical Journal, Nature Medicine among others. We are working with PAHO to put mirrored servers into every medical school in the Americas this year, with 5 years we should reach globally all medical schools. WHO has developed a Supercourse.
Initial pilot studies reveal that 2500 individuals will see each lecture each year, which is 50 times that of our classroom teaching. We have beta tested lectures in 2 centers in Japan and one in South Africa with very positive results. We are now developing a Chinese Heritage course.
PMCID: PMC1761712
10.  Security and privacy requirements for a multi-institutional cancer research data grid: an interview-based study 
Data protection is important for all information systems that deal with human-subjects data. Grid-based systems – such as the cancer Biomedical Informatics Grid (caBIG) – seek to develop new mechanisms to facilitate real-time federation of cancer-relevant data sources, including sources protected under a variety of regulatory laws, such as HIPAA and 21CFR11. These systems embody new models for data sharing, and hence pose new challenges to the regulatory community, and to those who would develop or adopt them. These challenges must be understood by both systems developers and system adopters. In this paper, we describe our work collecting policy statements, expectations, and requirements from regulatory decision makers at academic cancer centers in the United States. We use these statements to examine fundamental assumptions regarding data sharing using data federations and grid computing.
An interview-based study of key stakeholders from a sample of US cancer centers. Interviews were structured, and used an instrument that was developed for the purpose of this study. The instrument included a set of problem scenarios – difficult policy situations that were derived during a full-day discussion of potentially problematic issues by a set of project participants with diverse expertise. Each problem scenario included a set of open-ended questions that were designed to elucidate stakeholder opinions and concerns. Interviews were transcribed verbatim and used for both qualitative and quantitative analysis. For quantitative analysis, data was aggregated at the individual or institutional unit of analysis, depending on the specific interview question.
Thirty-one (31) individuals at six cancer centers were contacted to participate. Twenty-four out of thirty-one (24/31) individuals responded to our request- yielding a total response rate of 77%. Respondents included IRB directors and policy-makers, privacy and security officers, directors of offices of research, information security officers and university legal counsel. Nineteen total interviews were conducted over a period of 16 weeks. Respondents provided answers for all four scenarios (a total of 87 questions). Results were grouped by broad themes, including among others: governance, legal and financial issues, partnership agreements, de-identification, institutional technical infrastructure for security and privacy protection, training, risk management, auditing, IRB issues, and patient/subject consent.
The findings suggest that with additional work, large scale federated sharing of data within a regulated environment is possible. A key challenge is developing suitable models for authentication and authorization practices within a federated environment. Authentication – the recognition and validation of a person's identity – is in fact a global property of such systems, while authorization – the permission to access data or resources – mimics data sharing agreements in being best served at a local level. Nine specific recommendations result from the work and are discussed in detail. These include: (1) the necessity to construct separate legal or corporate entities for governance of federated sharing initiatives on this scale; (2) consensus on the treatment of foreign and commercial partnerships; (3) the development of risk models and risk management processes; (4) development of technical infrastructure to support the credentialing process associated with research including human subjects; (5) exploring the feasibility of developing large-scale, federated honest broker approaches; (6) the development of suitable, federated identity provisioning processes to support federated authentication and authorization; (7) community development of requisite HIPAA and research ethics training modules by federation members; (8) the recognition of the need for central auditing requirements and authority, and; (9) use of two-protocol data exchange models where possible in the federation.
PMCID: PMC2709611  PMID: 19527521
11.  Borderless Teleradiology with CHILI 
Teleradiology is one of the most evolved areas of telemedicine, but one of the basic problems which remains unsolved concerns system compatibility. The DICOM (Digital Imaging and Communications in Medicine) standard is a prerequisite, but it is not sufficient in all aspects. Examples of other currently open issues are security and cooperative work in synchronous teleconferences. Users without a DICOM radiological workstation would benefit from the ability to join a teleradiology network without any special tools. Drawbacks of many teleradiology systems are that they are monolithic in their software design and cannot be adapted to the actual user's environment. Existing radiological systems currently cannot be extended with additional software components. Consequently, every new application usually needs a new workstation with a different look and feel, which must be connected and integrated into the existing infrastructure.
This paper introduces the second generation teleradiology system CHILI. The system has been designed to match both the teleradiology requirements of the American College of Radiology (ACR), and the functionality and usability needs of the users. The experiences of software developers and teleradiology users who participated in the first years of the clinical use of CHILI's predecessor MEDICUS have been integrated into a new design. The system has been designed as a component-based architecture. The most powerful communication protocol for data exchange and teleconferencing is the CHILI protocol, which includes a strong data security concept. The system offers, in addition to its own secure protocol, several different communication methods: DICOM, classic e-mail, Remote Copy functions (RCP), File Transfer Protocol (FTP), the internet protocols HTTP (HyperText Transfer Protocol) and HTTPS (HyperText Transfer Protocol Secure),and CD-ROMs for off-line communication. These transfer methods allow the user to send images to nearly anyone with a computer and a network. The drawbacks of the non-CHILI protocols are that teleconferences are not possible, and that the user must take reasonable precautions for data privacy and security.
The CHILI PlugIn mechanism enables the users or third parties to extend the system capabilities by adding powerful image postprocessing functions or interfaces to other information systems. Suitable PlugIns can be either existing programs, or dedicated applications programmed with interfaces to the CHILI components. The developer may freely choose programming languages and interface toolkits.
The CHILI architecture is a powerful and flexible environment for Picture Archiving and Communications Systems (PACS)and teleradiology. More than 40 systems are currently running in clinical routine in Germany. More than 300,000 images have been distributed among the communication partners in the last two years. Feedback and suggestions from the users influenced the system architecture by a great extent. The proposed and implemented system has been optimized to be as platform independent, open, and secure as possible.
PMCID: PMC1761707  PMID: 11720917
Teleradiology; Telemedicine; Remote Consultation; Diagnostic Imaging; Computer-Assisted Image Interpretation; PACS; Middleware; TLS; Security; Plugin; Visualization
12.  Query by Browsing: An Alternative Hypertext Information Retrieval Method 
In this paper we discuss our efforts to develop programs which enhance the ability to navigate through large medical hypertext systems. Our approach organizes hypertext index terms into a belief network and uses reader feedback to update the degree of belief in the index terms' utility to a query. We begin by describing various possible configurations for indexes to hypertext. We then describe how belief network calculations can be applied to these indexes. After a brief discussion of early results using manuscripts from a medical handbook, we close with an analysis of our approach's applicability to a wider range of hypertext information retrieval problems.
PMCID: PMC2245610
13.  The Exam-Room Physician Workstation 
By combining and configuring commercially available hardware and software, we have developed a networked system of exam-room physician workstations that provides a platform for physician charting, medical reference, and patient education. The physical platform consists of IBM compatible computers and ethernet hardware. The software platform is a hypertext document management system called Idex distributed on a Novell network. Key features of the workstation include a graphical user interface, hypertext information access, network file-locking, and a document management shell. Clinical experience with the workstation suggests that patients accept the presence of a computer in the exam-room and that a hypertext medical record provides the speed of information access necessary for exam-room computing.
PMCID: PMC2245701
14.  eCAT: Online electronic lab notebook for scientific research 
eCAT is an electronic lab notebook (ELN) developed by Axiope Limited. It is the first online ELN, the first ELN to be developed in close collaboration with lab scientists, and the first ELN to be targeted at researchers in non-commercial institutions. eCAT was developed in response to feedback from users of a predecessor product. By late 2006 the basic concept had been clarified: a highly scalable web-based collaboration tool that possessed the basic capabilities of commercial ELNs, i.e. a permissions system, controlled sharing, an audit trail, electronic signature and search, and a front end that looked like the electronic counterpart to a paper notebook.
During the development of the beta version feedback was incorporated from many groups including the FDA's Center for Biologics Evaluation & Research, Uppsala University, Children's Hospital Boston, Alex Swarbrick's lab at the Garvan Institute in Sydney and Martin Spitaler at Imperial College. More than 100 individuals and groups worldwide then participated in the beta testing between September 2008 and June 2009. The generally positive response is reflected in the following quote about how one lab is making use of eCAT: "Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments."
By developing eCAT in close collaboration with lab scientists, Axiope has come up with a practical and easy-to-use product that meets the need of scientists to manage, store and share data online. eCAT is already being perceived as a product that labs can continue to use as their data management and sharing grows in scale and complexity.
PMCID: PMC2809322  PMID: 20334629
15.  CIS4/403: Design and Implementation of an Intranet-based system for Real-Time Tele-Consultation in Oncology 
This study describes a tele-consultation system (TCS) developed to provide a computing environment over a Wide Area Network (WAN) in North Italy (Province of Trento), that can be used by two or more physicians to share medical data and to work co-operatively on medical records. A pilot study has been carried out in oncology to assess the effectiveness of the system. The aim of this project is to facilitate the management of oncology patients by improving communication among the specialists of central and district hospitals.
Methods and Results
The TCS is an Intranet-based solution. The Intranet is based on a PC WAN with Windows NT Server, Microsoft SQL Server, and Internet Information Server. TCS is composed of native and custom applications developed in the Microsoft Windows (9x and NT) environment. The basic component of the system is the multimedia digital medical record, structured as a collection of HTML and ASP pages. A distributed relational database will allow users to store and retrieve medical records, accessed by a dedicated Web browser via the Web Server. The medical data to be stored and the presentation architecture of the clinical record had been determined in close collaboration with the clinicians involved in the project. TCS will allow a multi-point tele-consultation (TC) among two or more participants on remote computers, providing synchronized surfing through the clinical report. A set of collaborative and personal tools, whiteboard with drawing tools, point-to-point digital audio-conference, chat, local notepad, e-mail service, are integrated in the system to provide an user friendly environment. TCS has been developed as a client-server architecture. The client part of the system is based on the Microsoft Web Browser control and provides the user interface and the tools described above. The server part, running all the time on a dedicated computer, accepts connection requests and manages the connections among the participants in a TC, allowing multiple TC to run simultaneously. TCS has been developed in Visual C++ environment using MFC library and COM technology; ActiveX controls have been written in Visual Basic to perform dedicated tasks from the inside of the HTML clinical report. Before deploying the system in the hospital departments involved in the project, TCS has been tested in our laboratory by clinicians involved in the project to evaluate the usability of the system.
TCS has the potential to support a "multi-disciplinary distributed virtual oncological meeting". The specialists of different departments and of different hospitals can attend "virtual meetings" and interactively discuss on medical data. An expected benefit of the "virtual meeting" should be the possibility to provide expert remote advice from oncologists to peripheral cancer units in formulating treatment plans, conducting follow-up sessions and supporting clinical research.
PMCID: PMC1761746
Intranet; Teleconsultation; Oncology
16.  MED22/401: Hypertext Atlas For Pathology Education 
Macro- and microscopic pictures play the key role in the pathology diagnosis and education. Collections of annotated digital histological images are being prepared and an interface offering convenient way of dealing with high resolution images and their descriptions was developed. The atlas will be primary used in pre-graduate course of pathology at the University.
Leica DMLB microscope equipped with the Leica~S1 scanning camera is used to obtain pictures at the resolution of up to5112*5112 pixels, 3*12~bit color. These pictures are digitally manipulated (esp. contrast enhancement and sharpening), downsized to 3000*3000 pixels, 3*8 bit color and archived. Subsequently, these raw images are compressed using JPEG (JFIF lossy format) to 900*900 and 2000*2000 pixel images used in the actual collection. These pictures are logically glued together and described in the atlas source text prepared using the TeX/LaTeX typesetting system. LaTeX2HTML converter is used to produce the actual hypermedia document, while the same source can be used to obtain a more classical printed version of the atlas. The static character of the HTML hypertext document is made dynamic through JavaScript functions, which add the required interactivity.
The atlas is accessible using standard JavaScript enabled Web browsers. There is always one main window with the text, table of content, index, active section headers and other hypertext links, and links to individual images. All the images are displayed in separate windows. The 900*900 pixels images are used as standard resolution pictures, the higher resolution images (2000*2000) are displayed on demand in a separated ``magnifying glass'' window. This interface can be used to compare several pictures displaying them in the same time and providing also a tool to focus on the most important parts of the large windows. Use of the higher resolution images leads to no information loss through this process. The interface could mimic the fine focusing of the microscope that provided the picture and is a series of images taken in consecutive planes of focus.
The atlas was primary produced as a stand-alone package, stored on local disc or CD-ROM. In this form it is suitable for pre-graduate and initial postgraduate education. Currently, it is being converted into very flexible, easily available and expandable diagnostic tool available through Internet. The Internet accessible atlas may be easily updated and expanded with new images and text. Images at different compression levels could be stored, the low resolution one used to fast scan and the highest resolution images used for detailed comparison with unknown specimen. Through the very high speed network (e.g. TEN-155) it will be possible to transfer even the raw data images with resolution above3000*3000 pixels.
PMCID: PMC1761766
Pathology; Telepathology; Dermatopathology; Educational Technology; Multimedia
17.  Development, implementation and pilot evaluation of a Web-based Virtual Patient Case Simulation environment – Web-SP 
The Web-based Simulation of Patients (Web-SP) project was initiated in order to facilitate the use of realistic and interactive virtual patients (VP) in medicine and healthcare education. Web-SP focuses on moving beyond the technology savvy teachers, when integrating simulation-based education into health sciences curricula, by making the creation and use of virtual patients easier. The project strives to provide a common generic platform for design/creation, management, evaluation and sharing of web-based virtual patients. The aim of this study was to evaluate if it was possible to develop a web-based virtual patient case simulation environment where the entire case authoring process might be handled by teachers and which would be flexible enough to be used in different healthcare disciplines.
The Web-SP system was constructed to support easy authoring, management and presentation of virtual patient cases. The case authoring environment was found to facilitate for teachers to create full-fledged patient cases without the assistance of computer specialists. Web-SP was successfully implemented at several universities by taking into account key factors such as cost, access, security, scalability and flexibility. Pilot evaluations in medical, dentistry and pharmacy courses shows that students regarded Web-SP as easy to use, engaging and to be of educational value. Cases adapted for all three disciplines were judged to be of significant educational value by the course leaders.
The Web-SP system seems to fulfil the aim of providing a common generic platform for creation, management and evaluation of web-based virtual patient cases. The responses regarding the authoring environment indicated that the system might be user-friendly enough to appeal to a majority of the academic staff. In terms of implementation strengths, Web-SP seems to fulfil most needs from course directors and teachers from various educational institutions and disciplines. The system is currently in use or under implementation in several healthcare disciplines at more than ten universities worldwide. Future aims include structuring the exchange of cases between teachers and academic institutions by building a VP library function. We intend to follow up the positive results presented in this paper with other studies looking at the learning outcomes, critical thinking and patient management. Studying the potential of Web-SP as an assessment tool will also be performed.
More information about Web-SP:
PMCID: PMC1397827  PMID: 16504041
18.  Make it better but don't change anything 
With massive amounts of data being generated in electronic format, there is a need in basic science laboratories to adopt new methods for tracking and analyzing data. An electronic laboratory notebook (ELN) is not just a replacement for a paper lab notebook, it is a new method of storing and organizing data while maintaining the data entry flexibility and legal recording functions of paper notebooks. Paper notebooks are regarded as highly flexible since the user can configure it to store almost anything that can be written or physically pasted onto the pages. However, data retrieval and data sharing from paper notebooks are labor intensive processes and notebooks can be misplaced, a single point of failure that loses all entries in the volume. Additional features provided by electronic notebooks include searchable indices, data sharing, automatic archiving for security against loss and ease of data duplication. Furthermore, ELNs can be tasked with additional functions not commonly found in paper notebooks such as inventory control. While ELNs have been on the market for some time now, adoption of an ELN in academic basic science laboratories has been lagging. Issues that have restrained development and adoption of ELN in research laboratories are the sheer variety and frequency of changes in protocols with a need for the user to control notebook configuration outside the framework of professional IT staff support. In this commentary, we will look at some of the issues and experiences in academic laboratories that have proved challenging in implementing an electronic lab notebook.
PMCID: PMC2810290  PMID: 20098591
19.  HBVPathDB: A database of HBV infection-related molecular interaction network 
AIM: To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus’ and host’s genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection.
METHODS: The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML).
RESULTS: We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at
CONCLUSION: The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.
PMCID: PMC4305955  PMID: 15786551
Hepatitis B viruses; Pathway database; Molecular interactions
20.  Computers in imaging and health care: Now and in the future 
Journal of Digital Imaging  2000;13(4):145-156.
Early picture archiving and communication systems (PACS) were characterized by the use of very expensive hardware devices, cumbersome display stations, duplication of database content, lack of interfaces to other clinical information systems, and immaturity in their understanding of the folder manager concepts and workflow reengineering. They were implemented historically at large academic medical centers by biomedical engineers and imaging informaticists. PACS were nonstandard, home-grown projects with mixed clinical acceptance. However, they clearly showed the great potential for PACS and filmless medical imaging. Filmless radiology is a reality today. The advent of efficient softcopy display of images provides a means for dealing with the ever-increasing number of studies and number of images per study. Computer power has increased, and archival storage cost has decreased to the extent that the economics of PACS is justifiable with respect to film. Network bandwidths have increased to allow large studies of many megabytes to arrive at display stations within seconds of examination completion. PACS vendors have recognized the need for efficient workflow and have built systems with intelligence in the mangement of patient data. Close integration with the hospital information system (HIS)-radiology information system (RIS) is critical for system functionality. Successful implementation of PACS requires integration or interoperation with hospital and radiology information systems. Besides the economic advantages, secure rapid access to all clinical information on patients, including imaging studies, anytime and anywhere, enhances the quality of patient care, although it is difficult to quantify. Medical image management systems are maturing, providing access outside of the radiology department to images and clinical information throughout the hospital or the enterprise via the Internet. Small and medium-sized community hospitals, private practices, and outpatient centers in rural areas will begin realizing the benefits of PACS already realized by the large tertiary care academic medical centers and research institutions. Hand-held devices and the Worldwide Web are going to change the way people communicate and do business. The impact on health care will be huge, including radiology. Computer-aided diagnosis, decision support tools, virtual imaging, and guidance systems will transform our practice as value-added applications utilizing the technologies pushed by PACS development efforts. Outcomes data and the electronic medical record (EMR) will drive our interactions with referring physicians and we expect the radiologist to become the informaticist, a new version of the medical management consultant.
PMCID: PMC3453069  PMID: 11110253
picture archiving and communication systems (PACS); image storage and retrieval; folder manager; workflow manager; radiology information systems; computers; digital radiology
21.  Building a Virtual Network in a Community Health Research Training Program 
Objective: To describe the experiences, lessons, and implications of building a virtual network as part of a two-year community health research training program in a Canadian province.
Design: An action research field study in which 25 health professionals from 17 health regions participated in a seven-week training course on health policy, management, economics, research methods, data analysis, and computer technology. The participants then returned to their regions to apply the knowledge in different community health research projects. Ongoing faculty consultations and support were provided as needed. Each participant was given a notebook computer with the necessary software, Internet access, and technical support for two years, to access information resources, engage in group problem solving, share ideas and knowledge, and collaborate on projects.
Measurements: Data collected over two years consisted of program documents, records of interviews with participants and staff, meeting notes, computer usage statistics, automated online surveys, computer conference postings, program Web site, and course feedback. The analysis consisted of detailed review and comparison of the data from different sources. NUD*IST was then used to validate earlier study findings.
Results: The ten key lessons are that role clarity, technology vision, implementation staging, protected time, just-in-time training, ongoing facilitation, work integration, participatory design, relationship building, and the demonstration of results are essential ingredients for building a successful network.
Conclusion: This study provides a descriptive model of the processes involved in developing, in the community health setting, virtual networks that can be used as the basis for future research and as a practical guide for managers.
PMCID: PMC61441  PMID: 10887165
22.  The development of a client application for the collaborative social and medical services system. 
This paper describes the design and implementation of a client application for the Baylor College of Medicine Teen Health Clinics. The application is the front end to the Collaborative Social and Medical Services System (CSMSS) under development by Baylor's Medical Informatics and Computing Research Program [8]. The application provides distributed access to an underlying object oriented database system. A process driven and patient centered design will provide staff members with a complete set of services, including forms for data entry and viewing, query, and access management to facilitate efficient and effective delivery of services. Role-specific interfaces will be supplied for clerks, nurses, nurse practitioners, physicians, and social workers. The client application is being designed using object oriented methodologies and technologies with the C++ programming language, and will operate within a Microsoft Windows operating environment utilizing Object Linking and Embedding for application interoperability.
PMCID: PMC2247750  PMID: 7950000
23.  A novel collaborative e-learning platform for medical students - ALERT STUDENT 
BMC Medical Education  2014;14:143.
The increasing complexity of medical curricula would benefit from adaptive computer supported collaborative learning systems that support study management using instructional design and learning object principles. However, to our knowledge, there are scarce reports regarding applications developed to meet this goal and encompass the complete medical curriculum. The aim of ths study was to develop and assess the usability of an adaptive computer supported collaborative learning system for medical students to manage study sessions.
A study platform named ALERT STUDENT was built as a free web application. Content chunks are represented as Flashcards that hold knowledge and open ended questions. These can be created in a collaborative fashion. Multiple Flashcards can be combined into custom stacks called Notebooks that can be accessed in study Groups that belong to the user institution. The system provides a Study Mode that features text markers, text notes, timers and color-coded content prioritization based on self-assessment of open ended questions presented in a Quiz Mode. Time spent studying and Perception of knowledge are displayed for each student and peers using charts. Computer supported collaborative learning is achieved by allowing for simultaneous creation of Notebooks and self-assessment questions by many users in a pre-defined Group. Past personal performance data is retrieved when studying new Notebooks containing previously studied Flashcards. Self-report surveys showed that students highly agreed that the system was useful and were willing to use it as a reference tool.
The platform employs various instructional design and learning object principles in a computer supported collaborative learning platform for medical students that allows for study management. The application broadens student insight over learning results and supports informed decisions based on past learning performance. It serves as a potential educational model for the medical education setting that has gathered strong positive feedback from students at our school.
This platform provides a case study on how effective blending of instructional design and learning object principles can be brought together to manage study, and takes an important step towards bringing information management tools to support study decisions and improving learning outcomes.
PMCID: PMC4131539  PMID: 25017028
Medical education; Computer supported collaborative learning; E-learning; Information management; Memory retention; Computer-assisted instruction; Tailored learning; Student-centered learning; Spaced repetition
24.  A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC) 
Cancer Informatics  2007;3:255-274.
The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1) for bioinformatics and a repository of serum and tissue samples; (2) a data model for biomarker data storage; and (3) a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium’s intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer-specific biomarkers and encourage collaborative research efforts among the participating centers.
The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission.
The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual property/tech transfer agreements, and material transfer agreements that have been approved by each of the member institutions. This was the foundational work that has led to the development of a centralized data warehouse that has met each of the institutions’ IRB/HIPAA standards.
Currently, this “virtual biorepository” has over 58,000 annotated samples from 11,467 cancer patients available for research purposes. The clinical annotation of tissue samples is either done manually over the internet or semi-automated batch modes through mapping of local data elements with PCABC common data elements. The database currently holds information on 7188 cases (associated with 9278 specimens and 46,666 annotated blocks and blood samples) of prostate cancer, 2736 cases (associated with 3796 specimens and 9336 annotated blocks and blood samples) of breast cancer and 1543 cases (including 1334 specimens and 2671 annotated blocks and blood samples) of melanoma. These numbers continue to grow, and plans to integrate new tumor sites are in progress. Furthermore, the group has also developed a central web-based tool that allows investigators to share their translational (genomics/proteomics) experiment data on research evaluating potential biomarkers via a central location on the Consortium’s web site.
The technological achievements and the statewide informatics infrastructure that have been established by the Consortium will enable robust and efficient studies of biomarkers and their relevance to the clinical course of cancer. Studies resulting from the creation of the Consortium may allow for better classification of cancer types, more accurate assessment of disease prognosis, a better ability to identify the most appropriate individuals for clinical trial participation, and better surrogate markers of disease progression and/or response to therapy.
PMCID: PMC2675833  PMID: 19455246
25.  Supporting the "clinic without walls" with an event-directed messaging system integrated into an electronic medical record. 
To facilitate the communication of ideas, orders and treatment plans among providers practicing in a multidisciplinary ambulatory care setting, we have created an event-directed messaging system integrated into our larger Ambulatory Care Information System (ACIS). ACIS has been operational since 1992 and currently supports an average of 350 patient visits per day. The new messaging system permits a provider to send a message to the next provider who will be caring for a patient. The messages can be sent to any provider offering care in the future, or they can be directed to future visits with a particular clinical service. In contrast to traditional electronic mail systems, messages are not directed to specific providers or groups of provider. Messages are instead directed to a specific clinical event, namely a patient's visit to an appropriate clinic. Messages are displayed when a patient returns for a designated visit, both as part of a pre-printed progress note upon which a provider documents the visit and as part of a hypertext-based general information display in an electronic medical record. The messaging system helps providers ensure that subsequent providers caring for their patients will be alerted to pertinent aspects of a patient's care. It also similarly helps providers quickly gain familiarity with those issues prior providers had felt were important to highlight or did not want to risk being overlooked.
PMCID: PMC2233083  PMID: 8947746

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