Laboratory Notebooks Research Articles

Effective Integration of Informatics Tools to Enhance the Drug Discovery Process

Effective integration of data and laboratory informatics tools promises the ability for organizations to make better informed decisions about resource allocation during the drug discovery and development process, and for more informed decisions to be made with respect to the market opportunity for compounds. There are technologies on the horizon that could dramatically change how informatics organizations design, develop, deliver, and support applications and data infrastructures to deliver maximum value to drug discovery organizations. There are numerous benefits of integrating laboratory informatics tools like Laboratory Information Management System (LIMS), Chromatographic Data Systems (CDS), Electronic Laboratory Notebooks (ELN), and Analytical Instrumentation and Scientific Data Management Systems (SDMS) for drug discovery processes, but there is no well-established path for effective integration of these tools. We propose in this article four new integration models for effective integration of labor...

Development of a prediction model on the acceptance of electronic laboratory notebooks in academic environments

Documentation of research data plays a key role in the biomedical engineering innovation processes. It makes an important contribution to the protection of intellectual property, the traceability of results and fulfilling the regulatory requirement. Because of the increasing digitalization in laboratories, an electronic alternative to the commonly-used paper-bound notebooks could contribute to the production of sophisticated documentation. However, compared to in an industrial environment, the use of electronic laboratory notebooks is not widespread in academic laboratories. Little is known about the acceptance of an electronic documentation system and the underlying reasons for this. Thus, this paper aims to establish a prediction model on the potential preference and acceptance of scientists either for paper-based or electronic documentation. The underlying data for the analysis originate from an online survey of 101 scientists in industrial, academic and clinical environments. Various parameters were analyzed to identify crucial factors for the system preference using binary logistic regression. The analysis showed significant dependency between the documentation system preference and the supposed workload associated with the documentation system (p<0.006; odds ratio=58.543) and an additional personal component. Because of the dependency of system choice on specific parameters it is possible to predict the acceptance of an electronic laboratory notebook before implementation.

Biochemistry / Histone Protein Modification - Purdue University

The researcher is conducting research on the glial and neuronal cells of drosophila larvae, a genus of flies. She is examining changes in gene expression when nuclei lose histone-modifying complexes. The stages of her research involve a long period of methodology development, a shorter data collection period, and then data analysis. Various aspects of the data analysis are outsourced to facilities at the university. The lab notebook contains written documentation of all experiments and trials and links to data, versions of analysis and images, databases, and versions of the developing journal article. Therefore, keeping an organized electronic lab notebook is of high importance for the researcher. The centrality of the lab notebook to the function of the lab means that it is very important for her students to be trained to properly document their experiments using her lab notebook structures and protocols. There is a potential issue of being able to link some of the data files to the notebook because they are very large and must be stored at the analysis facility on campus.

LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory

BackgroundThe electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.Methodology/Principal FindingsWe 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.Conclusions/SignificanceLabTrove 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.

Implementation of an Electronic Laboratory Notebook to Accelerate Data Review in Bioanalysis

Electronic laboratory notebooks increase opportunities for collaboration and information exchange when compared with paper records. Depending on the degree of implementation, a laboratory- or enterprise-wide system can unify the collection, review and dissemination of data to improve laboratory efficiency and productivity. The advantages of an electronic laboratory notebook for speeding data review in bioanalysis are discussed, through the use of validated templates and organizational constructs to block errors in real-time and reduce manual audit tasks.

Implementation and Challenges of Electronic Notebooks

PPD, 2244 Dabney Road, Richmond, VA 23230, USA Tel.: +1 804 285 8414 E-mail: amy.pearsall@ppdi.com Electronic laboratory notebook (ELN) usage is growing in the bioanalysis industry. ELN vendors offer a variety of programmable templates that support multiple applications. The templates can vary from simple to complex. A development laboratory may only need a simple template that allows the scientist to electronically add free text to document their daily experiments. These experiments can be tagged to allow searchable access by others. This approach may minimize redundancy in the laboratory and allow easy access by multiple users at the same time. Other laboratories may want a customized approach that controls every step of the assay from start to finish. This approach can put limit checks on any method procedural step that is deemed critical, to ensure that potential errors are eliminated in advance. A simple template can be created quickly, whereas one that is complex will take significantly more time and involvement from multiple individuals [1]. Choosing a ELN vendor is most likely comparable to a drug company choosing a CRO. How long has the vendor been in business? Do they have a mature product? Have they been audited by the US FDA? Is the vendor accessible? Do they understand laboratory workflow and if not, can they be easily educated? ELN requires a symbiotic relationship. The vendor must become part of the team and do whatever is required to ensure the success of their product. A vendor must be flexible and willing to modify their product to work as needed in different environments [2]. In April 2009, PPD (VA, USA) chose Accelrys, Inc. (CA, USA; originally VelQuest Corporation) as a potential fit. Their company came to PPD in Richmond and evaluated all processes connected to laboratory operations. Laboratory staff (myself included) and instrument technology staff were given basic training on how to operate their programs. Basic procedures, such as use of the balance and pipette calibration, were evaluated. A simple analytical method with reagent preparations and extraction/injection templates was used as the test method. Accelrys, Inc. converted the analytical method into their SmartLab format and several pilot studies were conducted at PPD. The pilot studies proved that the vendor’s ELN product would be a good fit. PPD purchased the product in November 2009. In retrospect, choosing the vendor was easy. Laboratory support and participation were essential, so weekly and biweekly meetings with staff from multiple departments occurred for over a year. The individuals chosen were very knowledgeable about their processes. It is never easy to come to an agreement for change and PPD is no different. The difficulty escalates when there is change with options. The flexibility was there to have the ELN procedure flow in different scenarios. A simple example would be, when preparing a multicomponent reagent, do you add the small or large volume component first? The meetings could conclude with a perceived direction, only to meet the next time to find that someone had thought of another aspect that affected the agreed upon approach. Could decisions have been made faster with a smaller group of people? Absolutely, but key issues would have been overlooked. Compromise was required at some point by all and agreement on the initial ELN approach was achieved. In conjunction with the weekly meetings, other aspects were concurrently being addressed. In order to provide the ability to capture data throughout the laboratory, mobile devices and wireless technology were needed. Various types and sizes of laptops and tablets were evaluated Editorial SpEcial FocuS iSSuE: incrEaSing productivity

C&amp;EN Webinars - Electronic Lab Notebooks in the "First-to-File" Era: What Every R&amp;D Organization Needs to Know

C&amp;EN Webinars - Electronic Lab Notebooks in the "First-to-File" Era: What Every R&amp;D Organization Needs to Know

Vintage Physiology

Laboratory manuals, notebooks and instrumentation from Otto Warburg's Institute of Cell Physiology have been discovered at the Max Planck Institute of Biochemistry. Following Warburg's death in 1970 one of his technicians was transferred from Berlin-Dahlem to the newly founded biochemical institute at Martinsried near Munich, and brought with him these resources, which epitomize the singular position of Warburg's work style and institute in the 1950s and 1960s. Since the technician's skills and apparently outmoded instrumentation like the Warburg apparatus were still used in the context of 1970s membrane biochemistry, this trove also documents an unexpected continuity of research within the life sciences. Moreover, the service of Warburg's technician, which spans more than four decades, as well as the meticulous documentation of preparations and experiments, serve as a case in point for the importance of routine and rather mundane techniques in the post-war molecular life sciences.

A universal open-source Electronic Laboratory Notebook

Laboratory notebooks remain crucial to the activities of research communities. With the increase in generation of electronic data within both wet and dry analytical laboratories and new technologies providing more efficient means of communication, Electronic Laboratory Notebooks (ELN) offer equivalent record keeping to paper-based laboratory notebooks (PLN). They additionally allow more efficient mechanisms for data sharing and retrieval, which explains the growing number of commercial ELNs available varying in size and scope but all are increasingly accepted and used by the scientific community. The International Agency for Research on Cancer (IARC) having already an LIMS and a Biobank Management System for respectively laboratory workflows and sample management, we have developed a free multidisciplinary ELN specifically dedicated to work notes that will be flexible enough to accommodate different types of data. Information for installation of our freeware ELN with source codes customizations are detailed in supplementary data. Supplementary data are available at Bioinformatics online.

Architecture design of a user-orientated electronic laboratory notebook: A case study within an atmospheric chemistry community

Data is particularly valuable to scientists when details of its provenance are known. This research concerned deploying a user-orientated electronic laboratory notebook (ELN) system within a scientific community. The ELN system supported the capture and retrieval of semantic metadata describing the provenance of the modelling activities of scientists within that community. The research was grounded within the atmospheric chemistry community but has applicability to other communities using an iterative model development process. The ELN system involved the automatic capture of metadata concerning the modelling process together with inline annotations added by the modeller explaining the reasoning for modelling decisions at each step of the process. A full realisation of the ELN system was built and evaluated by members of the atmospheric chemistry community. In order to promote reusability the ELN system architecture had domain-independent as well as domain-dependent elements. An ontology (in OWL) was used to ensure that the specific terminology of the community was used within the provenance metadata and also that it was used consistently. Other domain-independent elements of the architecture included a dynamic graphic interface that allowed the modeller to view his/her modelling history. This was recorded as a set of nodes each pointing to the stored provenance metadata associated with a specific simulation run. In addition, there was an innovative mechanism that enabled the modeller to navigate through the various nodes. The navigation process supported making comparisons between different nodes: a facility that users found particularly valuable. Members of the atmospheric chemistry community took part in a two-day summative evaluation of the ELN system. This confirmed its value to the modellers and it is now being introduced more widely across the modelling community. In addition, the research proposes a methodology for transferring this ELN system to other modelling communities making use of the domain-independent elements of the architecture.

Electronic Laboratory Notebooks Progress and Challenges in Implementation

Electronic laboratory notebooks (ELNs) are increasingly replacing paper notebooks in life science laboratories, including those in industry, academic settings, and hospitals. ELNs offer significant advantages over paper notebooks, but adopting them in a predominantly paper-based environment is usually disruptive. The benefits of ELN increase when they are integrated with other laboratory informatics tools such as laboratory information management systems, chromatography data systems, analytical instrumentation, and scientific data management systems, but there is no well-established path for effective integration of these tools. In this article, we review and evaluate some of the approaches that have been taken thus far and also some radical new methods of integration that are emerging.

Practical Approach to Molecular Biology (PAMB): Sequential Experiments to Teach Basic Laboratory Skills

Students pursuing graduate degrees in the biomedical sciences require specific laboratory skills. We designed a course to teach these skills, ensuring uniformity and faster adaption in their education.AimTo test whether the course improved the technical ability and theoretical knowledge of first‐year graduate students.MethodsThe experiments were done sequentially—the results of each experiment leading to the next—and supplemented with lectures. Students learned about working safely in a laboratory, preparing solutions, keeping a laboratory notebook, and preparing a laboratory report, among other things; journal club discussion sessions and presentations were also included.ResultsPre– and post– self‐evaluations showed that students felt that the course addressed various deficiencies and enhanced their skills, an assessment supported by the course coordinator and supporting personnel, all of whom observed and subsequently evaluated student performance.ConclusionsThe PAMB course provides us with a tool to help incoming students better adapt to the PhD program, thereby improving the laboratory experience. This course generates data suitable for a written report, thus reinforcing presentation and scientific writing skills. We expect that this course will enhance the productivity and increase the success of the students in our PhD program. R25GM082406 &amp; 5G12RR003050/8G12MD007579

Retraction Note: Inhibition of RelA phosphorylation sensitizes chemotherapeutic agents-mediated apoptosis in constitutive NF-kappaB-expressing and chemoresistant cells

The corresponding author wishes to retract the above paper for the reason that the images in some of the Figure panels in the paper could not unambiguously be attributed in the laboratory notebooks.

Agassiz or Darwin: Faith and Science in Hemingway’s High School Zoology Class

An unresolved tension between faith and reason prevails in Hemingway’s work, but to fully comprehend this tension, we must first lay to rest the common misperception that his years at Oak Park High School lacked any significant introduction to Darwinian evolutionary theory and were instead dominated by the anti-evolutionary teachings of Louis Agassiz. This essay presents clear evidence to the contrary: Hemingway did indeed receive extensive exposure to Darwinian science in his high school zoology class in 1915–16. The truth lies in the very Darwinian textbook for the class as well as the fascinating laboratory notebook Hemingway kept for the course, which has gone largely unnoticed in the Monroe County Public Library in Key West.

The Aesthetics of Laboratory Inscription: Claude Bernard'sCahier Rouge

This essay explores the aesthetic sensibilities of the French physiologist Claude Bernard (1813-1878). In particular, it analyzes the Cahier Rouge (1850-1860), Bernard's acclaimed laboratory notebook. In this notebook, Bernard articulates the range of his experience as an experimental physiologist, juxtaposing without differentiation details of laboratory procedure and more personal queries, doubts, and reflections on experimentation, life, and art. Bernard's insights, it is argued, offer an aesthetic and phenomenological template for considering experimentation. His physiological point of view ranges from his own bodily aesthesis or sensory perception, through personal reflections on scientific discovery as an artistic process, to a broader metaphysical conception of life as an artistic creation. Such an aesthetic approach to physiology enables Bernard to reconcile his empirical methodology and his romantic idealism; it offers the history of laboratory science a framework for considering the individual, bodily, and emotional labor inherent in physiological experimentation.

Science in print: essays on the history of science and the culture of print

Ever since the threads of seventeenth-century natural philosophy began to coalesce into an understanding of the natural world, printed artifacts such as laboratory notebooks, research journals, college textbooks, and popular paperbacks have been instrumental to the development of what we think of today as 'science.' But just as the history of science involves more than recording discoveries, so too does the study of print culture extend beyond the mere cataloguing of books. In both disciplines, researchers attempt to comprehend how social structures of power, reputation, and meaning permeate both the written record and the intellectual scaffolding through which scientific debate takes place. Science in Print brings together scholars from the fields of print culture, environmental history, science and technology studies, medical history, and library and information studies. This ambitious volume paints a rich picture of those tools and techniques of printing, publishing, and reading that shaped the ideas and practices that grew into modern science, from the days of the Royal Society of London in the late 1600s to the beginning of the modern U.S. environmental movement in the early 1960s.

C&amp;EN Webinars - We Are Not a Pharma Company. Are Electronic Lab Notebooks for Us?

RETURN TO ISSUEPREVAdvertisementNEXTC&EN Webinars - We Are Not a Pharma Company. Are Electronic Lab Notebooks for Us?Cite this: Chem. Eng. News 2013, 91, 7, 46Publication Date (Print):February 18, 2013Publication History Published online31 March 2014Published inissue 18 February 2013https://doi.org/10.1021/cen-09107-ad20Copyright © 2013 Chemical & Engineering NewsArticle Views68Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (861 KB) Get e-Alerts

InChI in the wild: an assessment of InChIKey searching in Google

While chemical databases can be queried using the InChI string and InChIKey (IK) the latter was designed for open-web searching. It is becoming increasingly effective for this since more sources enhance crawling of their websites by the Googlebot and consequent IK indexing. Searchers who use Google as an adjunct to database access may be less familiar with the advantages of using the IK as explored in this review. As an example, the IK for atorvastatin retrieves ~200 low-redundancy links from a Google search in 0.3 of a second. These include most major databases and a very low false-positive rate. Results encompass less familiar but potentially useful sources and can be extended to isomer capture by using just the skeleton layer of the IK. Google Advanced Search can be used to filter large result sets. Image searching with the IK is also effective and complementary to open-web queries. Results can be particularly useful for less-common structures as exemplified by a major metabolite of atorvastatin giving only three hits. Testing also demonstrated document-to-document and document-to-database joins via structure matching. The necessary generation of an IK from chemical names can be accomplished using open tools and resources for patents, papers, abstracts or other text sources. Active global sharing of local IK-linked information can be accomplished via surfacing in open laboratory notebooks, blogs, Twitter, figshare and other routes. While information-rich chemistry (e.g. approved drugs) can exhibit swamping and redundancy effects, the much smaller IK result sets for link-poor structures become a transformative first-pass option. The IK indexing has therefore turned Google into a de-facto open global chemical information hub by merging links to most significant sources, including over 50 million PubChem and ChemSpider records. The simplicity, specificity and speed of matching make it a useful option for biologists or others less familiar with chemical searching. However, compared to rigorously maintained major databases, users need to be circumspect about the consistency of Google results and provenance of retrieved links. In addition, community engagement may be necessary to ameliorate possible future degradation of utility.

Towards Reusable Experiments: Making Metadata While You Measure

Event Abstract Back to Event Towards Reusable Experiments: Making Metadata While You Measure Shreejoy J. Tripathy1*, Anita De Waard2, Richard C. Gerkin1, David Marques2, Shawn D. Burton1 and Nathaniel N. Urban1 1 Carnegie Mellon University, Department of Biology, United States 2 Elsevier, Elsevier Labs, Netherlands Using research data acquired in other labs requires that the metadata, that define the conditions and manipulations of each experiment are well documented. Usually, this metadata is not stored with the experimental data itself, and is often written within the experimenter’s lab notebook and therefore is not easily searched or compiled. When scientists upload data files to a central repository (like crcns.org), metadata are often not included. For domain-specific databases (such as neuromorpho.org), metadata are added by expert curators in an expensive and painstaking process that does not scale up to the large amounts of scientific data produced every day. An effective way “scale-up” is to convince researchers to create digital metadata in real-time during their experiment. Here, we have developed an electronic lab notebook application (running on tablet computers and smartphones) to annotate in vitro electrophysiological recordings with essential methodological details. We tailored our system to the workflows used in the collection of electrophysiology data by the Urban, Gittis, and Barth Labs at Carnegie Mellon University. These labs study a variety of brain areas, addressing hypotheses from neural coding and synaptic plasticity to the mechanisms underlying neurological disorders; however, they share a core set of methodologies associated with recording neural activity from brain slices. Using the developed app, individual experimenters enter details (like the animal strain used or the neuron type recorded) through a series of drop-down menus (see Figure 1 for a screenshot). This structured data entry approach allows us to enforce a common metadata format and the usage of INCF standards and terminologies. Additionally, we designed the app’s interface to ensure simple, efficient data entry by the user. The collected metadata is uploaded directly to a relational database and combined with the acquired electrophysiology data files into a semantically-enriched, reusable format that allows for creative data exploration. This data can be used by the person collecting the data or others in the lab for testing hypotheses and analyzing collections of data from his or her own lab, in a web-based ‘Data-Dashboard’. Rather than being limited to datasets collected within a single lab, researchers can now find (using metadata as a search filter) and analyze relevant data collected in other labs. Through improving data organization, archiving, and sharing practices, this system will show clear benefits to the scientists performing and analyzing research data and, we hope, will empower demonstrably better neuroscience research. Figure 1 Acknowledgements This work was funded by the NIDCD (R01DC0005798) and Elsevier Research Data Services. Keywords: neuron electrophysiology, digital lab notebook, data sharing, experimental metadata, Reproducible Research Conference: Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013. Presentation Type: Oral presentation Topic: General neuroinformatics Citation: Tripathy SJ, De Waard A, Gerkin RC, Marques D, Burton SD and Urban NN (2013). Towards Reusable Experiments: Making Metadata While You Measure. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00051 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 08 Apr 2013; Published Online: 11 Jul 2013. * Correspondence: Mr. Shreejoy J Tripathy, Carnegie Mellon University, Department of Biology, Pittsburgh, PA, 15217, United States, stripat3@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Shreejoy J Tripathy Anita De Waard Richard C Gerkin David Marques Shawn D Burton Nathaniel N Urban Google Shreejoy J Tripathy Anita De Waard Richard C Gerkin David Marques Shawn D Burton Nathaniel N Urban Google Scholar Shreejoy J Tripathy Anita De Waard Richard C Gerkin David Marques Shawn D Burton Nathaniel N Urban PubMed Shreejoy J Tripathy Anita De Waard Richard C Gerkin David Marques Shawn D Burton Nathaniel N Urban Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Turning Experiments into Objects: The Cognitive Processes Involved in the Design of a Lab‐on‐a‐Chip Device

AbstractBackgroundIncreasingly, modern engineers are designing miniature devices that integrate complex activities, actions, processes, or operations involving many steps, persons, and equipment; a good example is a microfluidic lab‐on‐a‐chip device. The design of such devices is cognitively demanding and requires the generation of multiple model representations, which are used in an iterative fashion to analyze and improve prototype designs.PurposeThis study addresses two questions: How are various representations and prototypes used in the iterative design and building of a microfluidic lab‐on‐a‐chip device in a systems biology laboratory? In this design process, what cognitive functions did the representations serve?Design/MethodThis case study employed mixed methods. We utilized the standard ethnographic methods of participant observation, open‐ended interviewing of participants, and artifact collection in an integrated systems biology research lab. Data were analyzed using open and axial coding. We also used cognitive‐historical analysis to collect and analyze data from traditional historical sources (publications, grant proposals, laboratory notebooks, and technological artifacts) to recover how the salient representational, methodological, and reasoning practices were developed and used by the researchers.ResultsThe device design involved complex interactions among mental models, computational models, and building and testing prototypes; tagging and visualizations were used to query and validate the prototypes as well as the computational models; all these were integrated to meet stringent experimental and fabrication constraints. Integration takes place across many different kinds of representations. The building of external representations helped not just to off‐load cognitive load but also to add detail and constraints to the mental model.ConclusionsRepresentational fluency and flexibility are required to manage the complexity of modern bioengineered devices. To support the development of such fluency and flexibility, engineering students must understand the function and the use of such representations, an instructional goal that has implication for new models of learning.