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.
In a field study a new notebook design with adjustable screen was analyzed and compared to standard notebook position.
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.
This study demonstrates that notebooks with adjustable screen may be used to improve the posture. Future studies may focus on patients with musculoskeletal diseases.
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.
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 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.
ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicylate, a well-known inhibitor of MarR proteins and the ST1710 complex with its promoter DNA, refined to 1.8 and 2.10 Å resolutions, respectively. The ST1710–DNA complex shares the topology of apo-ST1710 and MarR proteins, with each subunit containing a winged helix-turn-helix (wHtH) DNA binding motif. Significantly large conformational changes occurred upon DNA binding and in each of the dimeric monomers in the asymmetric unit of the ST1710–DNA complex. Conserved wHtH loop residues interacting with the bound DNA and mutagenic analysis indicated that R89, R90 and K91 were important for DNA recognition. Significantly, the bound DNA exhibited a new binding mechanism.
Cannabinoid CB2 agonists produce antinociception without central nervous system (CNS) side-effects. This study was designed to characterize the pharmacological and antinociceptive profile of AM1710, a CB2 agonist from the cannabilactone class of cannabinoids. AM1710 did not exhibit off-target activity at 63 sites evaluated. AM1710 also exhibited limited blood brain barrier penetration. AM1710 was evaluated in tests of antinociception and CNS activity. CNS side-effects were evaluated in a modified tetrad (tail flick, rectal temperature, locomotor activity and rota-rod). Pharmacological specificity was established using CB1 (SR141716) and CB2 (SR144528) antagonists. AM1710 (0.1–10 mg/kg i.p.) produced antinociception to thermal but not mechanical stimulation of the hindpaw. AM1710 (5 mg/kg i.p.) produced a longer duration of antinociceptive action than the aminoalkylindole CB2 agonist (R,S)-AM1241 (1 mg/kg i.p.) at maximally antinociceptive doses. Antinociception produced by the low (0.1 mg/kg i.p.) dose of AM1710 was blocked selectively by the CB2 antagonist SR144528 (6 mg/kg i.p.), whereas antinociception produced by the high dose of AM1710 (5 mg/kg i.p.) was blocked by either SR144528 (6 mg/kg i.p.) or SR141716 (6 mg/kg i.p.). AM1710 did not produce hypoactivity, hypothermia, tail flick antinociception, or motor ataxia when evaluated in the tetrad at any dose. In conclusion, AM1710, a CB2-preferring cannabilactone, produced antinociception in the absence of CNS side-effects. Thus, any CB1-mediated antinociceptive effects of this compound may be attributable to peripheral CB1 activity. The observed pattern of pharmacological specificity produced by AM1710 is consistent with limited blood brain barrier penetration of this compound and absence of CNS side-effects.
cannabinoid; CB2; antinociception; tetrad; pain
Parental rearing behavior is a significant etiological factor for the vulnerability of psychopathology and has been an issue of clinical research for a long time. For this scope instruments are important who asses economically recalled parental rearing behavior in a clinical practice. Therefore, a short German instrument for the assessment of the recalled parental rearing behavior Fragebogen zum erinnerten elterlichen Erziehungsverhalten (FEE) was psychometrically evaluated [Recalled Parental Rearing Behavior].
This questionnaire was evaluated in a representative population sample (N = 2.948) in Germany which included 44.2% male and 55.8% female persons with a mean age of M = 47.35 (SD = 17.10, range = 18–92). For the content evaluation of the FEE the Life Satisfaction Questionnaire (FLZ) and the Inventory of Interpersonal Problems (IIP) was filled out by the participants.
The FEE scales yielded a good to satisfactory internal consistency and split-half reliability. Its three factors (rejection/punishment, emotional warmth, control/overprotection) correlated positively with most of the areas of life satisfaction. Furthermore, positive associations between interpersonal problems and parental rejection and control could be identified.
The FEE is a short, reliable and valid instrument that can be applied in the clinical practice. In addition, the data proved an association between recalled parental rearing behavior, life satisfaction and interpersonal problems conform to the literature. Finally, specific problems with the retrospective assessment of parental rearing behavior were addressed as well.
Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species.
We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described.
Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.
Design elements of clinical trials can introduce recruitment bias and reduce study efficiency. Trials involving the critically ill may be particularly prone to design-related inefficiencies. The VA/NIH Acute Renal Failure Trial Network (ATN) Study was designed to compare strategies of renal replacement therapy (RRT) in critically ill subjects with acute kidney injury (AKI).
Reasons for subject non-enrollment into the ATN Study were systematically monitored and categorized as modifiable or non-modifiable.
4339 subjects were screened; 2744 fulfilled inclusion criteria. Of these, 1034 were ineligible based on exclusion criteria. Of the remaining 1710 patients, 1124 (65.7%) enrolled. Impediments to informed consent excluded 21.4% of potentially eligible subjects; surrogate unavailability accounted for 1/3 of these exclusions. Delayed identification of potential subjects, physician refusal, and involvement in competing trials accounted for 4.4%, 2.7%, and 2.3% of exclusions. Comfort measures only (CMO) status, chronic illness, chronic kidney disease (CKD), and obesity excluded 11.8%, 7.8%, 7.6%, and 5.9% of potential subjects. Modification of an enrollment window reduced the loss of subjects from 6.6% to 2.3%.
The ATN Study’s enrollment efficiency compared favorably with previous ICU intervention trials and supports the representativeness of its enrolled population. Impediments to informed consent in the critically ill with AKI highlight the need for nontraditional acquisition methods. Restrictive enrollment windows may hamper subject recruitment, but can be effectively modified. The low rate of physician refusal acknowledges clinical equipoise in the study design. Underlying comorbidities are important design considerations for future trials involving the critically ill with AKI.
Acute Kidney Injury; Clinical Trial; Research Design; Recruitment; Enrollment; Critical Care; External Validity
Burkholderia pseudomallei is an intrinsically antibiotic-resistant Category B priority pathogen and the aetiological agent of melioidosis. Treatment of B. pseudomallei infection is biphasic and lengthy in order to combat the acute and chronic phases of the disease. Acute-phase treatment preferably involves an intravenous cephalosporin (ceftazidime) or a carbapenem (imipenem or meropenem). In this study, the anti-B. pseudomallei efficacy of a new monosulfactam, BAL30072, was tested against laboratory strains 1026b and 1710b and several isogenic mutant derivatives as well as a collection of clinical and environmental B. pseudomallei strains from Thailand. More than 93% of the isolates had minimal inhibitory concentrations (MICs) in the range 0.004–0.016 μg/mL. For the laboratory strain 1026b, the MIC of BAL30072 was 0.008 μg/mL, comparable with the MICs of 1.5 μg/mL for ceftazidime, 0.5 μg/mL for imipenem and 1 μg/mL for meropenem. Time–kill curves revealed that BAL30072 was rapidly bactericidal, killing >99% of bacteria in 2 h. BAL30072 activity was not significantly affected by efflux, it was only a marginal substrate of PenA β-lactamase, and activity was independent of malleobactin production and transport and the ability to transport pyochelin. In summary, BAL30072 has superior in vitro activity against B. pseudomallei compared with ceftazidime, meropenem or imipenem and it is rapidly bactericidal.
Burkholderia pseudomallei; Melioidosis; Therapy; Monosulfactam; Efflux; Siderophore
There are no treatments currently available for peanut allergy. Sublingual immunotherapy is a novel approach to the treatment of peanut allergy.
To investigate the safety, clinical effectiveness and immunologic changes with sublingual immunotherapy in peanut-allergic children.
In this double-blind, placebo-controlled study, subjects underwent 6 months of dose escalation and 6 months of maintenance dosing followed by a double-blind, placebo-controlled food challenge.
Eighteen children ages 1 to 11 years completed 12 months of dosing and the food challenge. Dosing side effects were primarily oropharyngeal and uncommonly required treatment. During the double-blind, placebo-controlled food challenge, the treatment group safely ingested 20 times more peanut protein than the placebo group (median 1710 mg vs. 85 mg, p=0.011). Mechanistic studies demonstrated a decrease in prick skin test wheal size (p=0.020) and decreased basophil responsiveness after stimulation with 10−2 mcg/ml (p=0.009) and 10−3 mcg/ml (p=0.009) of peanut. Peanut-specific IgE increased over the initial 4 months (p=0.002) then steadily decreased over the remaining 8 months (p=0.003) while peanut-specific IgG4 increased during the 12 months (p=0.014). Lastly, IL-5 levels decreased after 12 months (p=0.015). No statistically significant changes were found in IL-13 levels, the percent of T regulatory cells, or IL-10 and IFN-gamma production.
Peanut sublingual immunotherapy is able to safely induce clinical desensitization in peanut allergic children with evidence of immunologic changes suggesting a significant change in the allergic response. Further study is required to determine if continued peanut sublingual immunotherapy is able to induce long-term immune tolerance.
peanut allergy; sublingual immunotherapy; desensitization; food allergy
Intracellular Chlamydia (C.) bacteria cause in cattle some acute but rare diseases such as abortion, sporadic bovine encephalomyelitis, kerato-conjunctivitis, pneumonia, enteritis and polyarthritis. More frequent, essentially ubiquitous worldwide, are low-level, asymptomatic chlamydial infections in cattle. We investigated the impact of these naturally acquired infections in a cohort of 51 female Holstein and Jersey calves from birth to 15 weeks of age. In biweekly sampling, we measured blood/plasma markers of health and infection and analyzed their association with clinical appearance and growth in dependence of chlamydial infection intensity as determined by mucosal chlamydial burden or contemporaneous anti-chlamydial plasma IgM. Chlamydia 23S rRNA gene PCR and ompA genotyping identified only C. pecorum (strains 1710S, Maeda, and novel strain Smith3v8) in conjunctival and vaginal swabs. All calves acquired the infection but remained clinically asymptomatic. High chlamydial infection associated with reduction of body weight gains by up to 48% and increased conjunctival reddening (P<10−4). Simultaneously decreased plasma albumin and increased globulin (P<10−4) suggested liver injury by inflammatory mediators as mechanisms for the growth inhibition. This was confirmed by the reduction of plasma insulin like growth factor-1 at high chlamydial infection intensity (P<10−4). High anti-C. pecorum IgM associated eight weeks later with 66% increased growth (P = 0.027), indicating a potential for immune protection from C. pecorum-mediated growth depression. The worldwide prevalence of chlamydiae in livestock and their high susceptibility to common feed-additive antibiotics suggests the possibility that suppression of chlamydial infections may be a major contributor to the growth promoting effect of feed-additive antibiotics.
The reliability of clinical techniques to quantify thoracic spine rotation range of motion (ROM) has not been evaluated.
To determine the intratester and intertester reliability of 5 thoracic rotation measurement techniques.
Descriptive laboratory study.
University research laboratory.
Patients or Other Participants:
Forty-six healthy volunteers (age = 23.6±4.3 years, height = 171.0±9.6 cm, mass = 71.4 ±16.7 kg).
Main Outcome Measure(s):
We tested 5 thoracic rotation ROM techniques over 2 days: seated rotation (bar in back and front), half-kneeling rotation (bar in back and front), and lumbar-locked rotation. On day 1, 2 examiners obtained 2 sets of measurements (sessions 1, 2) to determine the within-session intertester reliability and within-day intratester reliability. A single examiner obtained measurements on day 2 (session 3) to determine the intratester reliability between days. Each technique was performed 3 times per side, and averages were used for data analysis. Reliability was determined using intraclass correlation coefficients, standard error of measurement (SEM), and minimal detectable change (MDC). Differences between raters during session 1 were determined using paired t tests.
Within-session intertester reliability estimates ranged from 0.85 to 0.94. Ranges for the SEM were 1.0° to 2.3° and for the MDC were 2.8° to 6.3°. No differences were seen between examiners during session 1 for seated rotation (bar in front, both sides), half-kneeling rotation (bar in front, left side), or the lumbar locked position (both sides) (all values of P > .05). Within-day intratester reliability estimates ranged from 0.86 to 0.95. Ranges for the SEM were 0.8° to 2.1° and for the MDC were 2.1 ° to 5. 9°. Between-days intratester reliability estimates ranged from 0.84 to 0.91. Ranges for the SEM were 1.4° to 2.0° and for the MDC were 3.9° to 5.6°.
All techniques had good reliability and low levels of measurement error. The seated rotation, bar in front, and lumbar-locked rotation tests may be used reliably when more than 1 examiner is obtaining measurements.
biomechanics; bubble inclinometer; goniometer; scapulothoracic joint
Chemotherapeutic agents produce dose-limiting peripheral neuropathy through mechanisms that remain poorly understood. We previously showed that AM1710, a cannabilactone CB2 agonist, produces antinociception without producing central nervous system (CNS)-associated side effects. The present study was conducted to examine the antinociceptive effect of AM1710 in rodent models of neuropathic pain evoked by diverse chemotherapeutic agents (cisplatin and paclitaxel). A secondary objective was to investigate the potential contribution of alpha-chemokine receptor (CXCR4) signaling to both chemotherapy-induced neuropathy and CB2 agonist efficacy.
AM1710 (0.1, 1 or 5 mg/kg i.p.) suppressed the maintenance of mechanical and cold allodynia in the cisplatin and paclitaxel models. Anti-allodynic effects of AM1710 were blocked by the CB2 antagonist AM630 (3 mg/kg i.p.), but not the CB1 antagonist AM251 (3 mg/kg i.p.), consistent with a CB2-mediated effect. By contrast, blockade of CXCR4 signaling with its receptor antagonist AMD3100 (10 mg/kg i.p.) failed to attenuate mechanical or cold hypersensitivity induced by either cisplatin or paclitaxel. Moreover, blockade of CXCR4 signaling failed to alter the anti-allodynic effects of AM1710 in the paclitaxel model, further suggesting distinct mechanisms of action.
Our results indicate that activation of cannabinoid CB2 receptors by AM1710 suppresses both mechanical and cold allodynia in two distinct models of chemotherapy-induced neuropathic pain. By contrast, CXCR4 signaling does not contribute to the maintenance of chemotherapy-induced established neuropathy or efficacy of AM1710. Our studies suggest that CB2 receptors represent a promising therapeutic target for the treatment of toxic neuropathies produced by cisplatin and paclitaxel chemotherapeutic agents.
Endocannabinoid; Cannabilactone; AM1710; Chemotherapy; Neuropathic pain; Chemokine; CXCR4; Mechanical allodynia; Cold allodynia; Hyperalgesia
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 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.
eCAT is an electronic lab notebook (ELN) developed by Axiope Limited. It is the first online ELN, the first ELN to be developed in close collaboration with lab scientists, and the first ELN to be targeted at researchers in non-commercial institutions. eCAT was developed in response to feedback from users of a predecessor product. By late 2006 the basic concept had been clarified: a highly scalable web-based collaboration tool that possessed the basic capabilities of commercial ELNs, i.e. a permissions system, controlled sharing, an audit trail, electronic signature and search, and a front end that looked like the electronic counterpart to a paper notebook.
During the development of the beta version feedback was incorporated from many groups including the FDA's Center for Biologics Evaluation & Research, Uppsala University, Children's Hospital Boston, Alex Swarbrick's lab at the Garvan Institute in Sydney and Martin Spitaler at Imperial College. More than 100 individuals and groups worldwide then participated in the beta testing between September 2008 and June 2009. The generally positive response is reflected in the following quote about how one lab is making use of eCAT: "Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments."
By developing eCAT in close collaboration with lab scientists, Axiope has come up with a practical and easy-to-use product that meets the need of scientists to manage, store and share data online. eCAT is already being perceived as a product that labs can continue to use as their data management and sharing grows in scale and complexity.
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
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.
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.
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).
software; resource management; resource sharing
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.
Darwin; Warm little pond; Origin of life; Spontaneous generation
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.
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.