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.
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.
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).
software; resource management; resource sharing
This study showed that an image data acquisition system connecting a high-speed camera or webcam to a notebook or personal computer (PC) can precisely capture most dominant modes of vibration signal, but may involve the non-physical modes induced by the insufficient frame rates. Using a simple model, frequencies of these modes are properly predicted and excluded. Two experimental designs, which involve using an LED light source and a vibration exciter, are proposed to demonstrate the performance. First, the original gray-level resolution of a video camera from, for instance, 0 to 256 levels, was enhanced by summing gray-level data of all pixels in a small region around the point of interest. The image signal was further enhanced by attaching a white paper sheet marked with a black line on the surface of the vibration system in operation to increase the gray-level resolution. Experimental results showed that the Prosilica CV640C CMOS high-speed camera has the critical frequency of inducing the false mode at 60 Hz, whereas that of the webcam is 7.8 Hz. Several factors were proven to have the effect of partially suppressing the non-physical modes, but they cannot eliminate them completely. Two examples, the prominent vibration modes of which are less than the associated critical frequencies, are examined to demonstrate the performances of the proposed systems. In general, the experimental data show that the non-contact type image data acquisition systems are potential tools for collecting the low-frequency vibration signal of a system.
image data acquisition; vibration signal; insufficient frame rate; time frequency analysis
Individuals with amnestic Mild Cognitive Impairment (MCI) have few empirically-based treatment options for combating their memory loss. This study sought to examine the efficacy of a calendar/notebook rehabilitation intervention, the Memory Support System (MSS), for individuals with amnestic MCI.
Forty individuals with single domain amnestic MCI and their program partners were randomized to receive the MSS, either with training or without (controls). Measures of adherence, activities of daily living, and emotional impact were completed at the first and last intervention session and again at 8-weeks and 6 months post intervention.
Training in use of a notebook/calendar system significantly improved adherence over those who received the calendars but no training. Functional ability and memory self efficacy significantly improved for those who received MSS training. Change in functional ability remained significantly better in the intervention group than in the control group out to 8 week follow up. Care partners in the intervention group demonstrated improved mood by 8 week and 6 month follow-up, while control care partners reported worse caregiver burden by 6 month follow up.
MSS training resulted in improvement in ADLs and sense of memory self efficacy for individuals with MCI. While ADL benefits were maintained out to 8 weeks post intervention, future inclusion of booster sessions may help extend the therapeutic effect out even further. Improved mood of care partners of trained individuals and worsening sense of caregiver burden over time for partners of untrained individuals further supports the efficacy of the MSS for MCI.
Mild Cognitive Impairment; Rehabilitation; Behavioral Intervention; Activities of Daily Living; Quality of Life; Caregivers
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.
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
The aim of this study was to analyze whether quiet standing posture is related to compensatory postural adjustment.
The latest data in clinical practice suggests that static posture may play a significant role in musculoskeletal function, even in dynamic activities. However, no evidence exists regarding whether static posture during quiet standing is related to postural adjustment.
Twenty healthy participants standing on a movable surface underwent unexpected, standardized backward and forward postural perturbations while kinematic data were acquired; ankle, knee, pelvis and trunk positions were then calculated. An initial and a final video frame representing quiet standing posture and the end of the postural perturbation were selected in such a way that postural adjustments had occurred between these frames. The positions of the body segments were calculated in these initial and final frames, together with the displacement of body segments during postural adjustments between the initial and final frames. The relationship between the positions of body segments in the initial and final frames and their displacements over this time period was analyzed using multiple regressions with a significance level of p ≤ 0.05.
We failed to identify a relationship between the position of the body segments in the initial and final frames and the associated displacement of the body segments.
The motion pattern during compensatory postural adjustment is not related to quiet standing posture or to the final posture of compensatory postural adjustment. This fact should be considered when treating balance disturbances and musculoskeletal abnormalities.
Static posture cannot predict how body segments will behave during compensatory postural adjustment.
Musculoskeletal Equilibrium; Posture; Movement; Biomechanics; Physical Therapy (Specialty)
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
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
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.
The problem of aesthetic perception occupied Vygotsky throughout his life. Working in different research collectives or networks he worked out different answers but never reached a final solution. Inadequate and incomplete access to his writings unfortunately hinders us from understanding Vygotsky’s ideas and his personal motives. Publication of his notebooks and unadulterated versions of his writings plus an analysis of his research networks will deepen our understanding.
Vygotsky; History of psychology; Aesthetics; Psychology of art
The paper tools used to monitor outreach work in all major cities in Viet Nam had substantial writing requirements for each contact with difficulty maintaining confidentiality.
This paper describes the development of a Unique Identifier Code (UIC), a field data collection notebook (databook) and a computer data entry system in Viet Nam. The databook can document 40 individual clients and has space for commodity distribution, group contacts and needles/syringe collection for each month.
Field implementation trials of the UIC and databook have been undertaken by more than 160 peer outreach workers to document their work with people who inject drugs (PWID) and sex workers (SW). Following an expanded trial in Hai Phong province, there have been requests for national circulation of the databook to be used by peer educators documenting outreach to PWID, SW and men who have sex with men. The standardized UIC and databook, in a variety of locally adapted formats, have now been introduced in more than 40 of the 63 provinces in Viet Nam.
This development in Viet Nam is, to our knowledge, the first example of the combination of a confidential UIC and an innovative, simple pocket-sized paper instrument with associated customized data-entry software for documenting outreach.
The quality of life analysis from the North East Japan 002 study is reported. Quality of life was maintained much longer in patients treated with gefitinib than in patients treated with standard chemotherapy.
For non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutations, first-line gefitinib produced a longer progression-free survival interval than first-line carboplatin plus paclitaxel but did not show any survival advantage in the North East Japan 002 study. This report describes the quality of life (QoL) analysis of that study.
Chemotherapy-naïve patients with sensitive EGFR-mutated, advanced NSCLC were randomized to receive gefitinib or chemotherapy (carboplatin and paclitaxel). Patient QoL was assessed weekly using the Care Notebook, and the primary endpoint of the QoL analysis was time to deterioration from baseline on each of the physical, mental, and life well-being QoL scales. Kaplan–Meier probability curves and log-rank tests were employed to clarify differences.
QoL data from 148 patients (72 in the gefitinib arm and 76 in the carboplatin plus paclitaxel arm) were analyzed. Time to defined deterioration in physical and life well-being significantly favored gefitinib over chemotherapy (hazard ratio [HR] of time to deterioration, 0.34; 95% confidence interval [CI], 0.23–0.50; p < .0001 and HR, 0.43; 95% CI, 0.28–0.65; p < .0001, respectively).
QoL was maintained much longer in patients treated with gefitinib than in patients treated with standard chemotherapy, indicating that gefitinib should be considered as the standard first-line therapy for advanced EGFR-mutated NSCLC in spite of no survival advantage.
Lung carcinoma; Epidermal growth factor receptor; EGFR; Tyrosine kinase inhibitor; TKI; Gefitinib; Quality of life; QoL
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.
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.
Lithium-ion secondary batteries are commonly used in electric vehicles, smart phones, personal digital assistants (PDA), notebooks and electric cars. These lithium-ion secondary batteries must charge and discharge rapidly, causing the interior temperature to rise quickly, raising a safety issue. Over-charging results in an unstable voltage and current, causing potential safety problems, such as thermal runaways and explosions. Thus, a micro flexible temperature sensor for the in in-situ monitoring of temperature inside a lithium-ion secondary battery must be developed. In this work, flexible micro temperature sensors were integrated into a lithium-ion secondary battery using the micro-electro-mechanical systems (MEMS) process for monitoring temperature in situ.
MEMS; micro temperature sensor; lithium-ion secondary battery; in situ monitoring
When Mary Cholmeley married Henry Fairfax in 1627, she carried to her new home in Yorkshire a leather-bound notebook filled with medical recipes. Over the next few decades, Mary and Henry, their children and various members of the Fairfax and Cholmeley families continually entered new medical and culinary information into this ‘treasury for health.’ Consequently, as it stands now, the manuscript can be read both as a repository of household medical knowledge and as a family archive. Focusing on two Fairfax ‘family books,’ this essay traces on the process through which early modern recipe books were created. In particular, it explores the role of the family collective in compiling books of knowledge. In contrast to past studies where household recipe books have largely been described as the products of exclusively female endeavors, I argue that the majority of early modern recipe collections were created by family collectives and that the members of these collectives worked in collaboration across spatial, geographical and temporal boundaries. This new reading of recipe books as testaments of the interests and needs of particular families encourages renewed examination of the role played by gender in the transmission and production of knowledge in early modern households.
Early modern medicine; gender history; household; informal science
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 http://genome.tugraz.at/iLAP/.
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.
Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment.
This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins.
ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.
Protein; Production; Purification; Reagent; Tracking; Prioritization; Web; Application
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.
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.
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.
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)
Field notes; notebooks; crowd sourcing; digitization; biodiversity; transcription; text-mining; Darwin Core; Junius Henderson; annotation; taxonomic referencing; natural history; Wikisource; Colorado; species occurrence records
The paralysis resulting from spinal cord injury severely limits voluntary seated-posture control and increases predisposition to a number of health risks. We developed and verified a musculoskeletal model of the hips and lumbar spine using published data. We then used the model to select the optimal muscles for—and evaluate the likely functional recovery benefit of—an 8-channel seated-posture-control neuroprosthesis based on functional electrical stimulation (FES). We found that the model-predicted optimal muscle set included the erector spinae, oblique abdominals, gluteus maximus, and iliopsoas. We mapped muscle excitations to seated trunk posture so that the required excitations at any posture could be approximated using a static map. Using the optimal muscle set, the model predicted a maximum stimulated range of motion of 49° flexion, 9° extension, and 16° lateral bend. In the nominal upright posture, the modeled user could hold almost 15 kg with arms at sides and elbows bent. We discuss in this article the practicality of using FES with the oblique abdominals. A seated-posture-control neuroprosthesis would increase the user’s bimanual work space and include several secondary benefits.
bimanual work space; biomechanics; functional electrical stimulation; musculoskeletal model; neuroprosthesis; posture control; rehabilitation; seated posture; spinal cord injury; trunk
OBJECTIVE: According to the literature, 30-70% of cyclists suffer from cervical, dorsal, or lumbar back pain. This study was conducted to evaluate one of the possible causes of low back pain and to suggest a solution by appropriate adjustments to the bicycle. METHODS: Serial fluoroscopic studies were performed while cyclists sat on different types of bicycle (sports, mountain, and city). Pelvic/spine angles were measured at different seat angles, and the related force vectors analysed. RESULTS: There was a tendency towards hyperextension of the pelvic/spine angle which resulted in an increase in tensile forces at the promontorium. These forces can easily be reduced by appropriate adjustment of the seat angle--that is, by creating an anterior inclining angle. The findings of the biomechanical analysis were then applied to a group of cyclists who were members of a cycling club and who complained of low back pain. After appropriate adjustment of the saddle angle, most of the cyclists (>70%) reported major improvement in the incidence and magnitude of their back pain. CONCLUSIONS: The incidence and magnitude of back pain in cyclists can be reduced by appropriate adjustment of the angle of the saddle. It is important that these findings be conveyed to cyclists, bicycle salesmen, trainers, and members of the general public who engage in cycling, in order to decrease the prevalence of back pain.