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1.  An Intelligent Terminal for Access to a Medical Database 
Very powerful data base management systems (DBMS) now exist which allow medical personnel access to patient record data bases. DBMS's make it easy to retrieve either complete or abbreviated records of patients with similar characteristics. In addition, statistics on data base records are immediately accessible. However, the price of this power is a large computer with the inherent problems of access, response time, and reliability. If a general purpose, time-shared computer is used to get this power, the response time to a request can be either rapid or slow, depending upon loading by other users. Furthermore, if the computer is accessed via dial-up telephone lines, there is competition with other users for telephone ports. If either the DBMS or the host machine is replaced, the medical users, who are typically not sophisticated in computer usage, are forced to learn the new system. Microcomputers, because of their low cost and adaptability, lend themselves to a solution of these problems. A microprocessor-based intelligent terminal has been designed and implemented at the USAF School of Aerospace Medicine to provide a transparent interface between the user and his data base. The intelligent terminal system includes multiple microprocessors, floppy disks, a CRT terminal, and a printer. Users interact with the system at the CRT terminal using menu selection (framing). The system translates the menu selection into the query language of the DBMS and handles all actual communication with the DBMS and its host computer, including telephone dialing and sign on procedures, as well as the actual data base query and response. Retrieved information is stored locally for CRT display, hard copy production, and/or permanent retention. Microprocessor-based communication units provide security for sensitive medical data through encryption/decryption algorithms and high reliability error detection transmission schemes.
Highly modular software design permits adapation to a different DBMS and/or host computer with only minor localized software changes. Importantly, this portability is completely transparent to system users. Although the terminal system is independent of the host computer and its DBMS, it has been linked to a UNIVAC 1108 computer supporting MRI's SYSTEM 2000 DBMS.
PMCID: PMC2231762
2.  The library's role in the continuing education of health professionals. 
Health sciences librarians have historically viewed disseminating information to health professionals as a major role. Typically, they have provided individualized services and are among the professions that help health professionals further their education after finishing formal education. Another group directly involved in health professional continuing education is continuing education (CE) providers who offer ongoing learning through group activities. These two professions often reached the same audiences in the past, and their different approaches--individual and group--were complementary. Health professionals who needed information immediately or who wished individual learning used the library while those who wanted to hear eminent colleagues tended to use CE meetings or seminars; some did both. The librarians and CE providers rarely interacted, but this is now changing. With the introduction of personal computers, medical librarians have expanded their responsibilities to include formalized classroom instruction. At the same time, CE providers have increased their scope beyond formalized group instruction into individualized education. Librarians and CE providers can either collaborate and share their expertise or they can compete against each other.
PMCID: PMC227763  PMID: 3450347
3.  Using GIS to establish a public library consumer health collection 
Learning the exact demographic characteristics of a neighborhood in which a public library serves, assists the collection development librarian in building an appropriate collection. Gathering that demographic information can be a lengthy process, and then formatting the information for the neighborhood in question becomes arduous.
As society ages and the methods for health care evolve, people may take charge of their own health. With this prospectus, public libraries should consider creating a consumer health collection to assist the public in their health care needs. Using neighborhood demographic information can inform the collection development librarians as to the dominant age groups, sex, and races within the neighborhood. With this information, appropriate consumer health materials may be assembled in the public library.
In order to visualize the demographics of a neighborhood, the computer program ArcView GIS (geographic information systems) was used to create maps for specified areas. The neighborhood data was taken from the U.S. Census Department's annual census and library addresses were accumulated through a free database. After downloading the census block information from the data was manipulated with ArcView GIS and queried to produce maps displaying the requested neighborhood demographics to view in respect to libraries.
ArcView GIS produced maps displaying public libraries and requested demographics. After viewing the maps the collection development librarian can see exactly what populations are served by the library and adjust the library's collection accordingly.
ArcView GIS can be used to produce maps displaying the communities that libraries serve, spot boundaries, be it "man-made or natural," that exist prohibiting customer service, and assist collection development librarians in justifying their purchases for a dedicated consumer health collection or resources in general.
PMCID: PMC535547  PMID: 15550171
4.  Work/training programs for international health science librarians in American medical school libraries. 
World understanding is more than a desirable goal today: it may be crucial to our survival. Many universities realize this and have in the past decade spent a great deal of time and money to ensure a steady flow of faculty and students between the U.S. and other countries. Librarians with faculty or academic status may benefit from promoting such relationships themselves. Job exchanges and training programs offer librarians in the United States the opportunity to become acquainted with their counterparts in other countries. Such programs enable librarians of various countries to become aware of one another's special needs and common problems, and allow them to share ideas and expertise. This paper presents an overview of international training programs for foreign librarians in the United States, focusing on programs for health sciences librarians in United States medical school libraries. Information is given on the availability and types of institutionally sponsored programs, as well as on MLA's Cunningham Fellowship Program. Some of the difficulties and the benefits of such programs are discussed.
PMCID: PMC227363  PMID: 2720220
5.  From both sides now: librarians' experiences at the Rocky Mountain Evidence-Based Health Care Workshop 
The Colorado Health Outcomes (COHO) Department of the School of Medicine at the University of Colorado Health Sciences Center (UCHSC) coordinates the Rocky Mountain Evidence-Based Health Care (EBHC) Workshop, which has been held annually since 1999. The goals of the workshop include helping participants—physicians, pharmacists, health care policy makers, journalists and librarians—learn and apply skills for critically appraising medical research literature and for effective use of evidence-based information resources. Participants are encouraged to share ideas and to plan local services and instruction for those working in clinical settings. Each year, librarians from UCHSC Denison Memorial Library participate as faculty by teaching searching skills (PubMed, Cochrane Library, ACP Journal Club, etc.), providing support to small groups, and staffing two computer labs. In 2002, Denison Library received a National Network of Libraries of Medicine (NN/LM) MidContinental Region Impact Award to fund the attendance of three health sciences librarians from the MidContinental Region, an academic education librarian, a clinical medical librarian, and a department librarian. In this paper, the participating librarians share the lessons they learned about how health care practitioners approach evidence-based practice. The participating librarians also share how they incorporated these lessons into their support of evidence-based practice related to teaching about evidence-based resources, assisting health care practitioners with developing answerable questions, enhancing the clinician-librarian partnership, and assisting practitioners in selecting evidence-based resources for quick answers to clinical questions.
PMCID: PMC314105  PMID: 14762465
6.  Faxon Finder/Faxon Xpress: report from a beta test site. 
In this environment of expanding information needs, spiraling journal costs, and curtailed financial resources, medical libraries must take advantage of the rapid evolution in document delivery services. There are exciting developments in transmission technology, from fax machines to scanners to the Internet. There is also a notable shift away from the traditional reliance on library networks toward use of commercial vendors as document providers. These changes require reevaluation of interlibrary loan (ILL) and document delivery systems on many levels, including pricing structures, work flow, and impact on collection development. As commercial vendors develop increasingly effective products, librarians can test, evaluate, and incorporate them into their ILL operations to enhance service to users and relieve the pressure to acquire new resources; in this way, librarians can move from the "just in case" practice of building an on-site collection to the "just in time" model of providing timely delivery of materials to users as needed. This paper describes a beta test of the Faxon Finder/Faxon Xpress table of contents and document delivery services conducted by the Treadwell Library of the Massachusetts General Hospital.
PMCID: PMC225891  PMID: 8004019
7.  Using Change Point Detection for Monitoring the Quality of Aggregate Data 
Data consisting of counts or indicators aggregated from multiple sources pose particular problems for data quality monitoring when the users of the aggregate data are blind to the individual sources. This arises when agencies wish to share data but for privacy or contractual reasons are only able to share data at an aggregate level. If the aggregators of the data are unable to guarantee the quality of either the sources of the data or the aggregation process then the quality of the aggregate data may be compromised.
This situation arose in the Distribute surveillance system (1). Distribute was a national emergency department syndromic surveillance project developed by the International Society for Disease Surveillance for influenza-like-illness (ILI) that integrated data from existing state and local public health department surveillance systems, and operated from 2006 until mid 2012. Distribute was designed to work solely with aggregated data, with sites providing data aggregated from sources within their jurisdiction, and for which detailed information on the un-aggregated ‘raw’ data was unavailable. Previous work (2) on Distribute data quality identified several issues caused in part by the nature of the system: transient problems due to inconsistent uploads, problems associated with transient or long-term changes in the source make up of the reporting sites and lack of data timeliness due to individual site data accruing over time rather than in batch. Data timeliness was addressed using prediction intervals to assess the reliability of the partially accrued data (3). The types of data quality issues present in the Distribute data are likely to appear to some extent in any aggregate data surveillance system where direct control over the quality of the source data is not possible. In this work we present methods for detecting both transient and long-term changes in the source data makeup.
We examined methods to detect transient changes in data sources, which manifest as classical outliers. We found that traditional statistical process control methods did not work well for detecting transient issues due to the presence of discontinuities cause by long term changes in the source makeup. As both transient and long-term changes in source makeup manifest as step changes, we examined the performance of change point detection methods for monitoring this data. These methods have been previously used for detecting changes in disease trends in data aggregated from Distribute (4). Following Kass-Hout (4), we used the Bayesian change point estimation procedure of Barry (5) as implemented in the R package BCP (6). We examined both offline and online detection using time series held at a constant lag.
We found that transient problems could be detected offline as neighboring change points with high posterior probability. When multiple outliers exist close together, detection can be improved by iteratively removing flagged data points and re-running the change point detection on the reduced data. Following the removal of outliers, remaining change points indicated long-term changes. To enable real-time monitoring for data quality problems we modified this offline detection process to in addition flag individual change points (rather than pairs of change points) detected in the most recent 5 days.
PMCID: PMC3692838
Data Quality; Surveillance; Changepoint methods; Distribute
8.  The UMLS project: making the conceptual connection between users and the information they need. 
Conceptual connections between users and information sources depend on an accurate representation of the content of available information sources, an accurate representation of specific user information needs, and the ability to match the two. Establishing such connections is a principal function of medical librarians. The goal of the National Library of Medicine's Unified Medical Language System (UMLS) project is to facilitate the development of conceptual connections between users and relevant machine-readable information. The UMLS model involves a combination of three centrally developed Knowledge Sources (a Metathesaurus, a Semantic Network, and an Information Sources Map) and a variety of smart interface programs that make use of these Knowledge Sources to help users in different environments find machine-readable information relevant to their particular practice or research problems. The third experimental edition of the UMLS Knowledge Sources was issued in the fall of 1992. Current priorities for the UMLS project include developing applications that make use of the Knowledge Sources and using feedback from these applications to guide ongoing enhancement and expansion of the Knowledge Sources. Medical librarians are involved heavily in the direction of the UMLS project, in the development of the Knowledge Sources, and in their experimental application. The involvement of librarians in reviewing, testing, and providing feedback on UMLS products will increase the likelihood that the UMLS project will achieve its goal of improving access to machine-readable biomedical information.
PMCID: PMC225759  PMID: 8472002
9.  Current status of information literacy instruction practices in medical libraries of Pakistan 
The research explored the current practices of information literacy (IL) instruction in medical libraries of Pakistan.
A semi-structured questionnaire was mailed to the head librarians of all 114 academic medical libraries in Pakistan. It investigated the types of IL instruction provided, topics covered, methods of delivery and assessment, level of integration in the curriculum, and level of collaboration with teaching staff.
The study revealed that 74% of the respondents had offered some types of IL instruction in their institutions during the previous year, ranging from library orientation to research-level skills. IL instruction is typically only offered to new students or first-time library users or on demand. A majority of the respondents developed IL instruction programs without faculty involvement. Librarians were primarily responsible for offering IL instruction in medical institutions. Face-to-face instruction in computer labs or lecture halls and individual instruction at reference desks were identified as the most common IL instruction delivery methods. The data indicated that oral feedback, written feedback, and searching in a computer lab were the most popular assessment methods that medical librarians used.
IL instruction activities in medical libraries of Pakistan are in their infancy. Medical librarians also lack systematic approaches to IL instruction.
Medical librarians need to develop educational partnerships with faculty for integrating IL instruction into the mainstream curriculum.
PMCID: PMC4188055  PMID: 25349546
10.  New activities and changing roles of health sciences librarians: a systematic review, 1990–2012 
The paper identifies and documents new health sciences librarian activities and roles during the period from 1990–2012.
A systematic review of the literature was conducted using MEDLINE, Library and Information Abstracts, Library Literature, Scopus, and Web of Science. To find new roles that might not yet have been described in the literature, job announcements published in the Medical Library Association email discussion list archives from 2008–2012 were searched. For inclusion, an article needed to contain a substantive description of a new role and/or activity performed by librarians and be in the field of medical or health sciences librarianship. Papers that did not describe an actual (rather than proposed) librarian role were excluded.
New roles identified through the literature search were: embedded librarians (such as clinical informationist, bioinformationist, public health informationist, disaster information specialist); systematic review librarian; emerging technologies librarian; continuing medical education librarian; grants development librarian; and data management librarian. New roles identified through job announcements were digital librarian, metadata librarian, scholarly communication librarian, and translational research librarian. New twists to old roles were also identified: clinical medical librarian, instruction librarian, outreach librarian, and consumer health librarian.
While the main purposes of health sciences librarianship remain the same, the new roles represent major new activities so that, for many librarians, daily on-the-job work is completely different.
This list of new activities should inform students contemplating medical librarianship careers, guide formal and continuing education programs, and encourage other librarians to consider these new services.
PMCID: PMC3794682  PMID: 24163598
11.  Librarians’ Role in Development and Achievement of Central Library Users’ Information Literacy (a Case Study: Iran) 
Materia Socio-Medica  2013;25(4):238-241.
Due to the development of technologies, communications, databases and information resource varieties in today’s information age, our various social, economic, cultural and political needs cannot be fulfilled by relying merely on past knowledge and skills as done previously. Information literacy (IL) as a set of necessary skills for all of us is an effective way of treating new technologies and their effective application in our lives. The study aimed to survey the library users’ views in the Central Library of Babol University of Medical Sciences (The Library), Iran, on the role and influences of librarians on their IL development and improvement.
This analytical survey used a researcher-made questionnaire for data collection. Research population consisted of all users referring Information Unit of The Library during 22 September - 20 December 2010. Of them, 150 users participating in at least 5 workshops held by The Library were selected as the study sample.
Based on the findings, 52.7 percent of the subjects rated the influence of the librarians on their IL development much and very much. 44.7 percent claimed that they more acquired IL skills from librarians rather than others. 100 (63.3%) subjects preferred workshops held by the librarian to other workshops.
The users of Information Unit of The Library perceived the training IL skills by librarians as a main influencing factor in their IL development and achievement. This emphasized the necessity of teaching IL to users and training the librarians in better teaching IL skills to library user.
PMCID: PMC3914755  PMID: 24511265
Information Literacy; Library Users; Librarians; Babol University of Medical Sciences; Iran.
12.  A pathway for hospital librarians: why is it vital? 
By the mid 2000s, reports of hospital librarians losing jobs and hospital libraries closing were rife. In 2005, Vital Pathways: The Hospital Libraries Project was established by 2005/06 MLA President M.J. Tooey, AHIP, FMLA, to assess the truth of these reports and to study and develop strategies to support hospital librarians. Throughout this long-term project, opportunities were sought to understand the issues more clearly.
A steering committee, along with three task forces, was established to carry out the work of the project. The steering committee provided oversight and had responsibility for promoting and marketing the project. The three task forces were responsible for conducting a survey on the status of hospital librarians, determining the involvement of librarians in medical education and accreditation, and researching and writing a document reviewing current and future roles for hospital librarians. Along the way, these responsibilities grew and evolved.
After a little more than three years, the Task Force on Vital Pathways for Hospital Librarians Steering Committee presented a final report regarding its accomplishments to the MLA Board of Directors. A sampling of these accomplishments includes the status of hospital librarians survey, a website, a position document with an accompanying executive summary, a short promotional brochure, and a final culminating activity, this symposium.
Although these are difficult times for all libraries, hospital librarians and libraries seem particularly affected. In a competitive health care environment that is driven by the bottom line, influenced by real estate hunger, and affected by the belief of hospital administrators that access to health information comes from the Internet and is free, the hospital librarian seems doomed. However, even in these difficult times, there are hospital librarians who are not only surviving, but thriving. Is it because they are entrepreneurial? Opportunistic? Innovative? Flexible? All of the above? None of the above? There are no clear predictors of success or of failure. However, the Vital Pathways Project has shed light on some of the issues and identified opportunities and strategies for the future.
PMCID: PMC2759155  PMID: 19851490
13.  The Controversy over Change * 
The full impact of twentieth century technology upon medical libraries was first felt in the late 1950s and early 1960s with the introduction of electronic automation into library methodology. During those years, often the aura of technology for the sake of technology prevailed, and medical librarians did little to inform themselves of capabilities, potentialities, and limitations in relation to cost-effective library usage of automation. Likewise, currently microforms and audiovisuals are frequently acquired for their own sake instead of for their capacity to transmit messages in the most effective and comprehensive way possible. Controversy has raged and still rages over the pros and cons of applying modern technology to library procedures and over the coexistence of the printed page with electronic media. New systems and methodologies, machine or manual, must realistically be evaluated in terms of increased service output by the library to its clientele. Regardless of technological sophistication, any machine that does not significantly contribute to that specific aim has no place in a library. The tradition of the medical librarian has always been to collect, organize, store, and disseminate information in the most efficient manner that the media of the times have had to offer.
PMCID: PMC225290  PMID: 75031
14.  Emerging roles for biomedical librarians: a survey of current practice, challenges, and changes 
This study is intended to (1) identify emerging roles for biomedical librarians and determine how common these roles are in a variety of library settings, (2) identify barriers to taking on new roles, and (3) determine how librarians are developing the capacity to take on new roles.
A survey was conducted of librarians in biomedical settings.
Most biomedical librarians are taking on new roles. The most common roles selected by survey respondents include analysis and enhancement of user experiences, support for social media, support for systematic reviews, clinical informationist, help for faculty or staff with authorship issues, and implementation of researcher profiling and collaboration tools. Respondents in academic settings are more likely to report new roles than hospital librarians are, but some new roles are common in both settings. Respondents use a variety of methods to free up time for new roles, but predominant methods vary between directors and librarians and between academic and hospital respondents. Lack of time is the biggest barrier that librarians face when trying to adopt new roles. New roles are associated with increased collaboration with individuals and/or groups outside the library.
Conclusion and Implications:
This survey documents the widespread incorporation of new roles in biomedical libraries in the United States, as well as the barriers to adopting these roles and the means by which librarians are making time for them. The results of the survey can be used to inform strategic planning, succession planning, library education, and career development for biomedical librarians.
PMCID: PMC3794683  PMID: 24163599
15.  A Grid-based solution for management and analysis of microarrays in distributed experiments 
BMC Bioinformatics  2007;8(Suppl 1):S7.
Several systems have been presented in the last years in order to manage the complexity of large microarray experiments. Although good results have been achieved, most systems tend to lack in one or more fields. A Grid based approach may provide a shared, standardized and reliable solution for storage and analysis of biological data, in order to maximize the results of experimental efforts. A Grid framework has been therefore adopted due to the necessity of remotely accessing large amounts of distributed data as well as to scale computational performances for terabyte datasets. Two different biological studies have been planned in order to highlight the benefits that can emerge from our Grid based platform. The described environment relies on storage services and computational services provided by the gLite Grid middleware. The Grid environment is also able to exploit the added value of metadata in order to let users better classify and search experiments. A state-of-art Grid portal has been implemented in order to hide the complexity of framework from end users and to make them able to easily access available services and data. The functional architecture of the portal is described. As a first test of the system performances, a gene expression analysis has been performed on a dataset of Affymetrix GeneChip® Rat Expression Array RAE230A, from the ArrayExpress database. The sequence of analysis includes three steps: (i) group opening and image set uploading, (ii) normalization, and (iii) model based gene expression (based on PM/MM difference model). Two different Linux versions (sequential and parallel) of the dChip software have been developed to implement the analysis and have been tested on a cluster. From results, it emerges that the parallelization of the analysis process and the execution of parallel jobs on distributed computational resources actually improve the performances. Moreover, the Grid environment have been tested both against the possibility of uploading and accessing distributed datasets through the Grid middleware and against its ability in managing the execution of jobs on distributed computational resources. Results from the Grid test will be discussed in a further paper.
PMCID: PMC1885859  PMID: 17430574
16.  Information-seeking behavior and use of information resources by clinical research coordinators 
Purpose: The study sought to understand the literature searching experiences and skills of clinical research coordinators at a large academic medical center.
Setting/Participants/Resources: The Health Sciences Library System, University of Pittsburgh, conducted a survey of clinical research coordinators at the University of Pittsburgh and the University of Pittsburgh Medical Center to solicit their perceived use and knowledge of the library's electronic resources.
Brief Description: The University of Pittsburgh Institutional Review Board (IRB) is a “high volume IRB” that monitors human subject research at both the University of Pittsburgh and the University of Pittsburgh Medical Center. More than 3,500 human research studies and clinical trials are active at any given time. Many studies entail more than minimal risk to human subjects, with the majority evaluating or including a drug or medical device. Clinical research coordinators are involved in most of these studies or trials. Their roles and responsibilities focus on managing many aspects of the study or clinical trial. As a first step in understanding the literature searching experiences and skills of these research coordinators, baseline data were gathered from this group in November 2004.
Results/Outcome: The data from this survey indicate that clinical research coordinators are a population who would benefit from training by academic medical center librarians in how to use electronic library resources and services.
Evaluation Method: A Web-based survey solicited participants' information (gender, education, job title) and role in the IRB process (job responsibilities, number studies they manage). The majority of the survey questions focused on the use of specific electronic library resources, the type of information wanted, and the types of problems encountered.
PMCID: PMC1324771  PMID: 16404469
17.  User-centered design and the development of patient decision aids: protocol for a systematic review 
Systematic Reviews  2015;4(1):11.
Providing patient-centered care requires that patients partner in their personal health-care decisions to the full extent desired. Patient decision aids facilitate processes of shared decision-making between patients and their clinicians by presenting relevant scientific information in balanced, understandable ways, helping clarify patients’ goals, and guiding decision-making processes. Although international standards stipulate that patients and clinicians should be involved in decision aid development, little is known about how such involvement currently occurs, let alone best practices. This systematic review consisting of three interlinked subreviews seeks to describe current practices of user involvement in the development of patient decision aids, compare these to practices of user-centered design, and identify promising strategies.
A research team that includes patient and clinician representatives, decision aid developers, and systematic review method experts will guide this review according to the Cochrane Handbook and PRISMA reporting guidelines. A medical librarian will hand search key references and use a peer-reviewed search strategy to search MEDLINE, EMBASE, PubMed, Web of Science, the Cochrane Library, the ACM library, IEEE Xplore, and Google Scholar. We will identify articles across all languages and years describing the development or evaluation of a patient decision aid, or the application of user-centered design or human-centered design to tools intended for patient use. Two independent reviewers will assess article eligibility and extract data into a matrix using a structured pilot-tested form based on a conceptual framework of user-centered design. We will synthesize evidence to describe how research teams have included users in their development process and compare these practices to user-centered design methods. If data permit, we will develop a measure of the user-centeredness of development processes and identify practices that are likely to be optimal.
This systematic review will provide evidence of current practices to inform approaches for involving patients and other stakeholders in the development of patient decision aids. We anticipate that the results will help move towards the establishment of best practices for the development of patient-centered tools and, in turn, help improve the experiences of people who face difficult health decisions.
Systematic review registration
PROSPERO CRD42014013241
Electronic supplementary material
The online version of this article (doi:10.1186/2046-4053-4-11) contains supplementary material, which is available to authorized users.
PMCID: PMC4328638  PMID: 25623074
Patient decision aids; Decision support; Shared decision-making; Patient education; Counseling; User-centered design; Human-centered design; Patient partnership; Stakeholder engagement; Implementation; Knowledge translation; Patient-centered care
18.  The IGOR Cloud Platform: Collaborative, Scalable, and Peer-Reviewed NGS Data Analysis 
Technical challenges facing researchers performing next-generation sequencing (NGS) analysis threaten to slow the pace of discovery and delay clinical applications of genomics data. Particularly for core laboratories, these challenges include: (1) Computation and storage have to scale with the vase amount of data generated. (2) Analysis pipelines are complex to design, set up, and share. (3) Collaboration, reproducibility, and sharing are hampered by privacy concerns and the sheer volume of data involved. Based on hands-on experience from large-scale NGS projects such as the 1000 Genomes Project, Seven Bridges Genomics has developed IGOR, a comprehensive cloud platform for NGS Data analysis that fully addresses these challenges: IGOR is a cloud-based platform for researchers and facilities to manage NGS data, design and run complex analysis pipelines, and efficiently collaborate on projects.Over a dozen curated and peer-reviewed NGS data analysis pipelines are publicly available for free, including alignment, variant calling, and RNA-Seq. All pipelines are based on open source tools and built to peer-reviewed specifications in close collaboration with researchers at leading institutions such as the Harvard Stem Cell Institute.Without any command-line knowledge, NGS pipelines can be built and customized in an intuitive graphical editor choosing from over 50 open source tools.When executing pipelines, IGOR automatically takes care of all resource management. Resources are seamlessly and automatically made available from Amazon Web Services and optimized for time and cost.Collaboration is facilitated through a project structure that allows researchers working in and across institutions to share files and pipelines. Fine-grained permissions allow detailed access control on a user-by-user basis for each project. Pipelines can be embedded and accessed through web pages akin to YouTube videos.Extensive batch processing and parallelization capabilities mean that hundreds of samples can be analyzed in the same amount of time that a single sample can be processed. Using file metadata, batch processing can be automated, e.g., by file, library, sample or lane.
The IGOR platform enables NGS research as a “turnkey” solution: Researchers can set up and run complex pipelines without expertise in command-line utilities or cloud computing. From a lab and facility perspective, the cloud-based architecture also eliminates the need to set up and maintain a large-scale infrastructure, typically resulting in at least 50% cost savings on infrastructure. By facilitating collaboration and easing analysis replication, the IGOR platform frees up the time of core laboratories to emphasize and focus on the research questions that ultimately guide them.
PMCID: PMC3635388
19.  UCMP and the Internet help hospital libraries share resources. 
The Medical Library Center of New York (MLCNY), a medical library consortium founded in 1959, has specialized in supporting resource sharing and fostering technological advances. In 1961, MLCNY developed and continues to maintain the Union Catalog of Medical Periodicals (UCMP), a resource tool including detailed data about the collections of more than 720 medical library participants. UCMP was one of the first library tools to capitalize on the benefits of computer technology and, from the beginning, invited hospital libraries to play a substantial role in its development. UCMP, beginning with products in print and later in microfiche, helped to create a new resource sharing environment. Today, UCMP continues to capitalize on new technology by providing access via the Internet and an Oracle-based search system providing subscribers with the benefits of: a database that contains serial holdings information on an issue specific level, a database that can be updated in real time, a system that provides multi-type searching and allows users to define how the results will be sorted, and an ordering function that can more precisely target libraries that have a specific issue of a medical journal. Current development of a Web-based system will ensure that UCMP continues to provide cost effective and efficient resource sharing in future years.
PMCID: PMC226583  PMID: 10427426
20.  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
21.  Mechanization of library procedures in a medium-sized medical library: XVI. Computer-assisted cataloging, the first decade. 
After ten years of experimentation in computer-assisted cataloging, the Washington University School of Medicine Library has decided to join the Ohio College Library Center network. The history of the library's work preceding this decision is reviewed. The data processing equipment and computers that have permitted librarians to explore different ways of presenting cataloging information are discussed. Certain cataloging processes are facilitated by computer manipulation and printouts, but the intellectual cataloging processes such as descriptive and subject cataloging are not. Networks and shared bibliographic data bases show promise of eliminating the intellectual cataloging for one book by more than one cataloger. It is in this area that future developments can be expected.
PMCID: PMC198912  PMID: 1148442
22.  Utilization of the medical librarian in a state Medicaid program to provide information services geared to health policy and health disparities 
Objective: The role of two solo medical librarians in supporting Medicaid programs by functioning as information specialists at regional and state levels is examined.
Setting: A solo librarian for the Massachusetts Medicaid (MassHealth) program and a solo librarian for the New England States Consortium Systems Organization (NESCSO) functioned as information specialists in context to support Medicaid policy development and clinical, administrative, and program staff for state Medicaid programs.
Brief Description: The librarian for MassHealth initially focused on acquiring library materials and providing research support on culturally competent health care and outreach, as part of the United States Department of Health and Human Services Culturally and Linguistically Appropriate Services in Health Care Standards. The NESCSO librarian focused on state Medicaid system issues surrounding the implementation of the Health Insurance Portability and Accountability Act. The research focus expanded for both the librarians, shaping their roles to more directly support clinical and administrative policy development. Of note, the availability and dissemination of information to policy leaders facilitated efforts to reduce health disparities. In Massachusetts, this led to a state legislative special commission to eliminate health disparities, which released a report in November 2005. On a regional level, the NESCSO librarian provided opportunities for states in New England to share ideas and Medicaid program information. The Centers for Medicaid and Medicare are working with NESCSO to explore the potential for using the NESCSO model for collaboration for other regions of the United States.
Results/Outcomes: With the increased attention on evidence-based health care and reduction of health disparities, medical librarians are called on to support a variety of health care information needs. Nationally, state Medicaid programs are being called on to provide coverage and make complex medical decisions regarding the delivery of benefits. Increasing numbers of beneficiaries and shrinking Medicaid budgets demand effective and proactive decision making to provide quality care and to accomplish the missions of state Medicaid programs. In this environment, the opportunities for information professionals to provide value and knowledge management are increasing.
PMCID: PMC1435841  PMID: 16636710
23.  Team building with information system departments: a hospital librarian's experience in coexisting, collaborating, and cooperating. 
Hospital librarians and information systems (IS) staff regard themselves as information professionals and have coexisted in the same institutions for many years. While hospital librarians have increased their computer literacy, IS staff have begun to recognize the value of knowledge-based information as an IS resource. Parallel growth and mutual interest have resulted in increased opportunities for information professionals to share skills and network for mutual advantage. Creating positive relationships between the hospital librarian and IS staff can be critical to the success of the hospital library. This paper provides a framework in which to explore the levels of relationship that exist within institutions between hospital librarians and IS staff. The "knowing/caring ladder" is presented as a model to illustrate levels of relationship and their consequences. The authors contend that recognition of the levels of professional relationship determines the success or failure of team building.
PMCID: PMC299402  PMID: 8826623
24.  Improving access to knowledge-based health sciences information: early results from a statewide collaborative effort. 
Access to biomedical literature has been shown to reduce the patient's length of stay and thus reduce the cost of the hospital visit. Unfortunately, access to the most current information, at the time and place of need, requires a substantial commitment of resources in the form of staff expertise, computer hardware and software, and user training. The cost of these resources may be prohibitively high for all but the largest institutions. The Arizona Health Information Network (AZHIN) brings together librarians, information systems specialists, and health care professionals from hospitals throughout the state in an effort to share resources and expertise. By reducing the cost of access, AZHIN has increased the availability of health-related information across the state. Progress in AZHIN's first two years is described.
PMCID: PMC226240  PMID: 9160149
25.  The impact of IAIMS on the work of information experts. Integrated Advanced Information Management Systems. 
Integrated Advanced Information Management Systems (IAIMS) programs differ but have certain characteristics in common. Technological and organizational integration are universal goals. As integration takes place, what happens to those implementing the vision? A survey of 125 staff members, or information experts, involved in information or informatics at an IAIMS-funded institution was conducted during the last year of the implementation phase. The purpose was to measure the impact of IAIMS on the jobs of those in the library and related service units, and the computing, telecommunications, and health informatics divisions. The researchers used newly developed scales measuring levels of integration (knowledge of and involvement with other departments), customer orientation (focus on the user), and informatedness (changes in the nature of work beyond automation of former routines). Ninety-four percent of respondents indicated that their jobs had changed a great deal; the changes were similar regardless of division. To further investigate the impact of IAIMS on librarians in particular, a separate skills survey was conducted. The IAIMS librarians indicated that technology and training skills are especially needed in the new, integrated environment.
PMCID: PMC226064  PMID: 8547905

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