Related Articles

Background

Professional working at computer notebooks is associated with high requirements on the body posture in the seated position. By the high continuous static muscle stress resulting from this position at notebooks, professionals frequently working at notebooks for long hours are exposed to an increased risk of musculoskeletal complaints. Especially in subjects with back pain, new notebooks should be evaluated with a focus on rehabilitative issues.

Methods

In a field study a new notebook design with adjustable screen was analyzed and compared to standard notebook position.

Results

There are highly significant differences in the visual axis of individuals who are seated in the novel notebook position in comparison to the standard position. Also, differences are present between further alternative notebook positions. Testing of gender and glasses did not reveal influences.

Conclusion

This study demonstrates that notebooks with adjustable screen may be used to improve the posture. Future studies may focus on patients with musculoskeletal diseases.

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.

Part diary, part scientific record, biological field notebooks often contain details necessary to understanding the location and environmental conditions existent during collecting events. Despite their clear value for (and recent use in) global change studies, the text-mining outputs from field notebooks have been idiosyncratic to specific research projects, and impossible to discover or re-use. Best practices and workflows for digitization, transcription, extraction, and integration with other sources are nascent or non-existent. In this paper, we demonstrate a workflow to generate structured outputs while also maintaining links to the original texts. The first step in this workflow was to place already digitized and transcribed field notebooks from the University of Colorado Museum of Natural History founder, Junius Henderson, on Wikisource, an open text transcription platform. Next, we created Wikisource templates to document places, dates, and taxa to facilitate annotation and wiki-linking. We then requested help from the public, through social media tools, to take advantage of volunteer efforts and energy. After three notebooks were fully annotated, content was converted into XML and annotations were extracted and cross-walked into Darwin Core compliant record sets. Finally, these recordsets were vetted, to provide valid taxon names, via a process we call “taxonomic referencing.” The result is identification and mobilization of 1,068 observations from three of Henderson’s thirteen notebooks and a publishable Darwin Core record set for use in other analyses. Although challenges remain, this work demonstrates a feasible approach to unlock observations from field notebooks that enhances their discovery and interoperability without losing the narrative context from which those observations are drawn.

“Compose your notes as if you were writing a letter to someone a century in the future.”

Perrine and Patton (2011)

The Journey Project, part of the Virginia Commonwealth University Libraries' Social Work Information Specialist in Context Fellowship, was designed to merge social work and consumer health librarianship skills in order to improve the provision of health information to patients. A resource notebook was created encompassing the many dimensions of cancer health information. A social work informationist distributed the notebooks and provided individualized consultations with respect to patients' health information needs. Areas of congruence as well as key differences between social work and consumer health librarianship emerged during the course of the project. Merging the two professions into the role of a social work informationist increased the ability to attend holistically to clients' health information needs.

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.

Background

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.

Results

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."

Conclusion

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.

Currently most biomedical labs in universities and government funded research institutions use paper lab notebooks for recording experimental data and spreadsheets for managing sample data. One consequence is that sample management and documenting experiments are viewed as separate and distinct activities, notwithstanding that samples and aliquots are an integral part of a majority of the experiments carried out by these labs.

Various drivers are pushing labs towards integrated management of sample data and experimental data. These include the ever increasing amounts of both kinds of data, the increasing adoption of online collaborative tools, changing expectations about online communication, and the increasing affordability of electronic lab notebooks and sample management software. There is now an opportunity for smaller labs, which have been slow to move from paper to electronic record keeping, to leapfrog better resourced commercial labs and lead the way in adopting the new generation of tools which permit integrated management of samples and experimental data and a range of tangible benefits to conducting research, including:

1. Fewer lost and mislabelled samples

2. Clearer visualization of relationships between samples and experiments

3. Reduction of experimental error

4. More effective search

5. Productivity gains

6. More efficient use of freezers, leading to cost reduction and enhanced sustainability

7. Improved archiving and enhanced memory at the lab and institutional levels

Background

MeduMobile was a project to develop and evaluate learning scenarios for medical students and teachers by use of video communication and notebooks. Its core part was assigned to various medical routines, conferences or meetings such as doctor-patient bedside conversation. These were filmed by video teams and broadcasted live via the WLAN of the Charité campus to course participating students. One type of the learning arrangements was the autopsy conference as an on-call scenario.

Materials and methods

The MeduMobile project consisted of two main compartments: the regular seminar event which took place every week or month, and the on-call event. For an on-call event the students were informed two hours before the lesson's start. A mobile video team organised the video conference via a specific MeduMobile seminar system. This software offered the students to log. The MeduMobile seminar system is based on the Windows operating system and realises an extended video communication via WLAN. Thirteen access points were implemented at the Charité Campus Virchow Klinikum and Campus Mitte. A questionnaire was developed to investigate in the response and learning effect of the mobile seminar system.

Results

During the MeduMobile project 42 video conferences with (cumulative) 145 participating students took place. Four autopsy conferences could be organised as on-call scenarios within this project. A prospective, not randomised follow-up study was included 25 students of the 1st – 6th clinical semester. According to the answers, professional reasoning, professional performance, sustainability, and the complexity were broadly accepted by the students.

Discussion

In principle, the MeduMobile realised an interdisciplinary case presentation using video conference and web page. The evaluation indicates a high acception of such complex case presentation with multidisciplinary settings. The use of the notebooks in mobile learning enables an interconnective training and promotes a complex learning.

This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.

This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp).

OBJECTIVE: Because anecdotal evidence indicates that the behaviour of cars (and their drivers) with respect to bicycles is highly variable, this study was undertaken to determine whether car colour correlates with the space allowed by the driver for passing a bicycle. DESIGN: Randomized recollection. SETTING: The streets of Vancouver and Burnaby, BC. PARTICIPANTS: The author, her bike, lots of cars and a few transit buses. METHODS: For a 10-day period in the summer of 1998, the investigator attempted, while cycling, to remember car colours and associated behaviours until she reached her various destinations. Data were eventually recorded in a tattered spiral-bound notebook saved from university days. OUTCOME MEASURES: Numbers of cars in 2 categories: "good" (those that gave extra space to cyclists) and "bad" (those that didn't). RESULTS: Read the article to find out. CONCLUSION: Although there was a slightly greater chance that a passing car would give a cyclist extra space, riders should be especially cautious when they catch sight of white and maroon vehicles.

When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that “the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable”. Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organic compounds could lead to the appearance of organisms. Although he favored the possibility that life could appear by natural processes from simple inorganic compounds, his reluctance to discuss the issue resulted from his recognition that at the time it was possible to undertake the experimental study of the emergence of life.

The University of Minnesota Medical School has an innovative curriculum, called Didactic/Selective, which provides third- and fourth-year medical students with multidisciplinary and multispecialty courses. Within this framework, the Bio-Medical Library planned a course to teach the knowledge and skills necessary for library research and information management. It included (1) searching case-related topics in print indexes, (2) formulating and processing MEDLINE searches on BRS Colleague, (3) building a personal file with PC-File or Notebook, and (4) exploring various methods for current awareness. Students' evaluations were positive, with the majority indicating that they found the course interesting and the knowledge gained substantial.

Background

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.

Results

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 http://genome.tugraz.at/iLAP/.

Conclusion

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.

It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate description of order in nature, and by about 1780 it had been largely abandoned without a satisfactory alternative having been agreed upon. In 1750 Donati described aquatic and terrestrial organisms as forming a network, and a few years later Buffon depicted a network of genealogical relationships among breeds of dogs. In 1764 Bonnet asked whether the Chain might actually branch at certain points, and in 1766 Pallas proposed that the gradations among organisms resemble a tree with a compound trunk, perhaps not unlike the tree of animal life later depicted by Eichwald. Other trees were presented by Augier in 1801 and by Lamarck in 1809 and 1815, the latter two assuming a transmutation of species over time. Elaborate networks of affinities among plants and among animals were depicted in the late Eighteenth and very early Nineteenth centuries. In the two decades immediately prior to 1837, so-called affinities and/or analogies among organisms were represented by diverse geometric figures. Series of plant and animal fossils in successive geological strata were represented as trees in a popular textbook from 1840, while in 1858 Bronn presented a system of animals, as evidenced by the fossil record, in a form of a tree. Darwin's 1859 tree and its subsequent elaborations by Haeckel came to be accepted in many but not all areas of biological sciences, while network diagrams were used in others. Beginning in the early 1960s trees were inferred from protein and nucleic acid sequences, but networks were re-introduced in the mid-1990s to represent lateral genetic transfer, increasingly regarded as a fundamental mode of evolution at least for bacteria and archaea. In historical context, then, the Network of Life preceded the Tree of Life and might again supersede it.

Reviewers

This article was reviewed by Eric Bapteste, Patrick Forterre and Dan Graur.

The means we use to record the process of carrying out research remains tied to the concept of a paginated paper notebook despite the advances over the past decade in web based communication and publication tools. The development of these tools offers an opportunity to re-imagine what the laboratory record would look like if it were re-built in a web-native form. In this paper I describe a distributed approach to the laboratory record based which uses the most appropriate tool available to house and publish each specific object created during the research process, whether they be a physical sample, a digital data object, or the record of how one was created from another. I propose that the web-native laboratory record would act as a feed of relationships between these items. This approach can be seen as complementary to, rather than competitive with, integrative approaches that aim to aggregate relevant objects together to describe knowledge. The potential for the recent announcement of the Google Wave protocol to have a significant impact on realizing this vision is discussed along with the issues of security and provenance that are raised by such an approach.

Objective

To assess the effects of web-based care management on glucose and blood pressure control over 12 months in patients with poorly controlled diabetes mellitus.

Research Design and Methods

104 patients with diabetes mellitus and hemoglobin A1c ≥ 9.0% who received their care at a VA medical center were recruited. All participants completed a diabetes education class and were randomized to continue with usual care (n = 52) or receive web-based care management (n = 52). The care management group received a notebook computer, glucose and blood pressure monitoring devices and access to a care management website. The website provided educational modules, accepted uploads from monitoring devices, and had an internal messaging system for patients to communicate with the care manager.

Results

Participants receiving web-based care management had lower hemoglobin A1c over 12 months (P<0.05) when compared to education and usual care. Persistent website users had greater improvement in hemoglobin A1c when compared to intermittent users (−1.9% vs. −1.2%, P=0.051) or education and usual care (−1.4%, P<0.05). Greater numbers of website data uploads were associated with larger declines in hemoglobin A1c (highest tertile −2.1%, lowest tertile: −1.0%, P<0.02). Hypertensive participants in the web-based care management group had a greater reduction in systolic blood pressure (P<0.01). HDL cholesterol rose and triglycerides fell in the web-based care management group (P<0.05).

Conclusions

Web-based care management may be a useful adjunct in the care of patients with poorly controlled diabetes mellitus.

In an effort to design a simulation environment that is more similar to that of neurophysiology, we introduce a virtual slice setup in the NEURON simulator. The virtual slice setup runs continuously and permits parameter changes including changes to synaptic weights and time course and to intrinsic cell properties. The virtual slice setup permits shocks to be applied at chosen locations and activity to be sampled intra- or extracellularly from chosen locations. By default, a summed population display is shown during a run to indicate the level of activity and no states are saved. Simulations can run for hours of model time, therefore it is not practical to save all of the state variables which in any case are primarily of interest at discrete times when experiments are being run: the simulation can be stopped momentarily at such times to save activity patterns. The virtual slice setup maintains an automated notebook showing shocks and parameter changes as well as user comments. We demonstrate how interaction with a continuously running simulation encourages experimental prototyping and can suggest additional dynamical features such as ligand wash-in and wash-out – alternatives to typical instantaneous parameter change. The virtual slice setup currently uses event-driven cells and runs at approximately 2 minutes/hour on a laptop.

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.

This paper describes the design and implementation of a pen-based computer system for remote preoperative data collection. The system is envisaged to be used by anaesthesia staff at different hospital scenarios where pre-operative data are generated. Pen-based technology offers important advantages in terms of portability and human-computer interaction, as direct manipulation interfaces by direct pointing, and "notebook user interfaces metaphors". Being the human factors analysis and user interface design a vital stage to achieve the appropriate user acceptability, a methodology that integrates the "usability" evaluation from the earlier development stages was used. Additionally, the selection of a pen-based computer system as a portable device to be used by health care personnel allows to evaluate the appropriateness of this new technology for remote data collection within the hospital environment. The work presented is currently being realised under the Research Project "TANIT: Telematics in Anaesthesia and Intensive Care", within the "A.I.M.--Telematics in Health CARE" European Research Program.

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.

We are developing a networked resource for the National Library of Medicine's Unified Medical Language System. We call this resource the UMLS Retriever, which is an instance of our VNS Retriever architecture. Our prototype user interface makes use of the Virtual Notebook System Browser. The development of a networked UMLS service will result in numerous advantages to our user community.

As part of our effort to create an Integrated Academic Information Management System at Baylor College of Medicine, we are developing information technology to support the efforts of scientific work groups. Many of our ideas in this regard are embodied in a system called the Virtual Notebook which is intended to facilitate information sharing and management in such groups. Here we discuss the foundations of that system - a hypertext system that we have developed using a relational data base and the distributable interface the we have written in the X Window System.

This paper describes the design of RS/1,™ the Research System, and its use in clinical patient studies. RS/1 is an interactive computer software system developed by the Medical Systems Group at BBN.

Investigators and technicians who have never before used computers can learn RS/1 with a few hours of training. It uses familiar and intuitive concepts for data handling and data analysis, such as the “automated notebook” format of data storage, the direct use of graphs in curve-fitting, and a simple command language.

Its versatility has made RS/1 useful in clinical research contexts, especially for studies involving patient care data.

Individuals with amnestic Mild Cognitive Impairment (MCI) currently have few treatment options for combating their memory loss. The Memory Support System (MSS) is a calendar and organization system with accompanying 6-week curriculum designed for individuals with progressive memory impairment. Ability to learn the MSS and its utility were assessed in 20 participants. Participants were significantly more likely to successfully use the calendar system after training. Ninety-five percent were compliant with the MSS at training completion, and 89% continued to be compliant at follow-up. Outcome measures revealed a medium effect size for improvement in functional ability. Subjects further reported improved independence, self-confidence, and mood. This initial examination of the MSS suggests that with appropriate training, individuals with amnestic MCI can and will use a memory notebook system to help compensate for memory loss. These results are encouraging that the MSS may help with the symptoms of memory decline in MCI.