Laboratory Notebooks Research Articles

High School students conduct research on the neonatal immune response as part of the Students and Teachers As Research Scientists (STARS) program

Abstract The Students and Teachers As Research Scientists (STARS) program offers academically-talented high school students in the Saint Louis metropolitan area an opportunity to do research in a variety of scientific fields. Fourteen students have been mentored in my immunology laboratory during the last 9 summers as a part of the STARS program. Students take on small-scale, hypothesis-driven independent projects related to the neonatal immune response of respiratory viral infection using a mouse model. The high school students take basic safety training, blood borne pathogen training and biohazard animal training within the first few days of the program. Each student learns the basic mouse model and then specific techniques (immunostaining, western blot analysis, qPCR and flow cytometry) needed to test to their hypothesis. Students learn how to keep laboratory notebooks, how to find and read primary journal articles, and basic laboratory skills. While the main goal of the program is to teach the scientific process, other structured activities include lectures by nationally-known scientists, information concerning the higher education admissions process, and social activities. The program culminates with a written research paper and a short powerpoint presentation. The papers are written in the style of a peer-reviewed journal article in the field of immunology; each student receives assistance in writing from the primary mentor and from a STARS advisor. Since its inception in 1987, the STARS program has sent on more than 2,000 students with research experience to top universities.

The MPO system for automatic workflow documentation

Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for critical applications. However, it is not the mere existence of data that is important, but our ability to make use of it. Experience has shown that when metadata is better organized and more complete, the underlying data becomes more useful. Traditionally, capturing the steps of scientific workflows and metadata was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing, and annotation. This paper presents the Metadata, Provenance, and Ontology (MPO) System, the software that can automate the documentation of scientific workflows and associated information. Based on recorded metadata, it provides explicit information about the relationships among the elements of workflows in notebook form augmented with directed acyclic graphs. A set of web-based graphical navigation tools and Application Programming Interface (API) have been created for searching and browsing, as well as programmatically accessing the workflows and data. We describe the MPO concepts and its software architecture. We also report the current status of the software as well as the initial deployment experience.

Research for All: Large Introductory Laboratory Classes Investigate the Evolutionary Conservation of Metabolic Pathways

The explosion of genomic sequence information, particularly for microbial organisms, presents opportunities to engage large numbers of undergraduate students in authentic research within regular laboratory classes. The Pathways over Time project was designed as a semester‐long research investigation in which students investigate the phylogenetic conservation of enzymes involved in a metabolic pathway. The project was designed to teach students core concepts of molecular biology, including evolution, structure/function relationships, information transfer, energy transformation and systems biology. Other course goals include the application of the scientific process, quantitative analysis, and the use of databases and bioinformatics tools.Each semester, 150–200 students enroll in 12 parallel sections of BIOL2040, Investigations in Molecular Cell Biology. Working in teams of three, students study the conservation of enzymes involved in methionine biosynthesis between the budding yeast, S. cerevisiae, and the fission yeast, Schizosaccharomyces pombe, species separated by close to a billion years of evolution. Methionine biosynthesis in yeast involves several multi‐enzyme pathways, which are subject to a variety of regulatory controls. Working in teams of three, students become “experts” on one particular MET gene as they learn the basic techniques of microbiology, bioinformatics, molecular cell biology and genetics. The rapid pace of the course does not allow students to repeat experiments. Instead, students post their data to a data‐sharing wiki site to determine if their results are reproducible.Student learning is assessed with pre‐lab quizzes, lab notebooks, oral and poster presentations, database and literature assignments, and a series of “micro‐reports” that are assembled into a final research report in the format of a scientific publication. Pre‐and post‐course evaluation instruments include concept tests and self‐assessed confidence and learning gains. Assessment data indicate significant gains on all measures.The Pathways over Time project was designed with sustainability in mind. The project can be easily adapted to other organisms and enzyme systems, depending on instructor experience and interest. The three elements required for course design are a multi‐gene system to study, a genetically‐tractable organism for complementation analyses, and a test organism with a sequenced genome. At Boston College, for example, students have successfully demonstrated the conservation of multiple MET gene functions between S. cerevisiae and S. pombe. Moving forward, Boston College will use a new test organism in which MET gene function has been predicted from DNA sequence comparisons, but function has not been tested by complementation.Support or Funding InformationNational Science Foundation grant 114028

A tool for reproducible research: From data analysis (in R) to a typeset laboratory notebook (as .pdf) using the text editor Emacs with the 'mp' package

SoftwareMuch scientific research makes use of commonly available 'office' software. While numerous more fully-featured open-source alternatives exist, the integration of diverse tools and platforms which their use often entails can be challenging. The mp package for Emacs aims to bring together a number of these elements with the goal of simplifying the process of converting an .R file, as used for data analysis, to a nicely formatted .pdf which includes the complete description of the methods and interpretation. We discuss the rationale for development of the package and illustrate its applications and options with a series of experiments from our laboratory.Experimental workWe demonstrate the inhibitory effects of the ketone body \emph{beta}-hydroxybutyrate (BHB) on the growth and motility of a cancer cell line. BHB is produced endogenously; levels may be increased in certain medial conditions e.g. diabetic ketoacidosis. They may also be raised voluntarily e.g. by adopting the ketogenic diet. BHB is known to inhibit the growth of other neoplastic cell lines. However the finding that it can do so in a cell line selected for their propensity to metastasize to the brain is novel. Given the challenges in treating patients with melanoma metastatic to brain, this work strengthens the rationale for investigating the ketogenic diet as a potential adjunct to treatment in such cases.

Beyond blank slates in the lab notebook

Chemistry![Figure][1] PHOTO: MEDIAPHOTOS/ISTOCK PHOTO Keeping an accurate laboratory notebook is a critical element of good scientific practice. It's helpful to start at an early age, so Willoughby et al. explored the influence of the reporting format on the record kept by undergraduates (and in one case more experienced researchers) conducting several chemistry experiments. Specifically, they focused on how templates, both paper-based and computer-based, affected the quantity and quality of information captured. They found that section headings and contextual cues helped ensure the preservation of a certain essential subset of information. At the same time, a free-form reporting format led to more detailed explanatory discussion of observations. J. Cheminform. 10.1186/s13321-016-0118-6 (2016). [1]: pending:yes

9th GCC closed forum: CAPA in regulated bioanalysis; method robustness, biosimilars, preclinical method validation, endogenous biomarkers, whole blood stability, regulatory audit experiences and electronic laboratory notebooks.

The 9th GCCClosed Forum was held just prior to the 2015 Workshop on Recent Issues in Bioanalysis (WRIB) in Miami, FL, USA on 13 April 2015. In attendance were 58 senior-level participants, from eight countries, representing 38 CRO companies offering bioanalytical services. The objective of this meeting was for CRO bioanalytical representatives to meet and discuss scientific and regulatory issues specific to bioanalysis. The issues selected at this year's closed forum include CAPA, biosimilars, preclinical method validation, endogenous biomarkers, whole blood stability, and ELNs. A summary of the industry's best practices and the conclusions from the discussion of these topics is included in this meeting report.

Effects of using structured templates for recalling chemistry experiments.

BackgroundThe way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interface for the capture of experiment records through the use of forms and templates. These templates can be useful by providing cues to help researchers to remember to record particular aspects of their experiment, but they may also constrain the information that is recorded by encouraging them to record only what is asked for. It is therefore unknown whether using structured templates for capturing experiment records will have positive or negative effects on the quality and usefulness of the records for assessment and future use. In this paper we report on the results of a set of studies investigating the effects of different template designs on the recording of experiments by undergraduate students and academic researchers.ResultsThe results indicate that using structured templates to write up experiments does make a significant difference to the information that is recalled and recorded. These differences have both positive and negative effects, with templates prompting the capture of specific information that is otherwise forgotten, but also apparently losing some of the personal elements of the experiment experience such as observations and explanations. Other unexpected effects were seen with templates that can change the information that is captured, but also interfere with the way an experiment is conducted.ConclusionsOur results showed that using structured templates can improve the completeness of the experiment context information captured but can also cause a loss of personal elements of the experiment experience when compared with allowing the researcher to structure their own record. The results suggest that interfaces for recording information about chemistry experiments, whether paper-based questionnaires or templates in Electronic Laboratory Notebooks, can be an effective way to improve the quality of experiment write-ups, but that care needs to be taken to ensure that the correct cues are provided.Graphical abstractScientists have traditionally recorded their research in paper notebooks, a format that provides great flexibility for capturing information. In contrast, Electronic Laboratory Notebooks frequently make use of forms or structured templates for capturing experiment records. Structured templates can provide cues that can improve record quality by increasing the amount of information captured and encouraging consistency. However, using the wrong cues can lead to a loss of personal elements of the experiment experience and frustrate users. This image shows two participants from one of our studies recording their experiment using a computer-based templateElectronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0118-6) contains supplementary material, which is available to authorized users.

Notice of Retraction.

HomeCirculation ResearchVol. 118, No. 3Notice of Retraction Free AccessRetractionPDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citationsPermissions ShareShare onFacebookTwitterLinked InMendeleyReddit Jump toFree AccessRetractionPDF/EPUBNotice of Retraction Originally published5 Feb 2016https://doi.org/10.1161/RES.0000000000000090Circulation Research. 2016;118:e31This article is retracted byAngiotensin II–Inducible Smooth Muscle Cell Apoptosis Involves the Angiotensin II Type 2 Receptor, GATA-6 Activation, and FasL-Fas EngagementTan NY, Li J-M, Stocker R, Khachigian LM. Angiotensin II-Inducible Smooth Muscle Cell Apoptosis Involves the Angiotensin II Type 2 Receptor, GATA-6 Activation, and FasL-Fas Engagement. Circ Res. 2009;105:422–430; doi: 10.1161/CIRCRESAHA.109.203323After being made aware of concerns related to Figures 6C and 6E in the above article, the University of New South Wales (UNSW) commissioned an independent, external report to examine this issue.In this article, Figure 6C (middle lower panel) was described as a section of a carotid from a rat treated with Ang II+GATA 6 siRNA and stained with antibodies to GATA-6. Figure 6E (lower right panel) is described as a section of a carotid from a different rat treated with Ang II+ Negative Control siRNA and stained with IgG. Upon further examination, it was determined that Figure 6C and Figure 6E appear to be identical except that the image in Figure 6C shows the presence of a number of darker nuclei.As part of their investigation, UNSW was unable to locate any electronic record of the original images and was unable to locate any records of the images in original lab books. The original slides have degraded over time and it was not possible to verify the authenticity of the images. The independent report, however, found that related quantitative data were recorded in the original lab books. Although the independent report commissioned by UNSW was unable to reach a definitive conclusion regarding this issue, the original concerns regarding these figures remain.UNSW has not attributed any instance of research misconduct or responsibility for the unavailability of the original data to Professor Khachigian or to any of the authors of the publication.Based on the unresolvable concerns with these figures, the editors, therefore, hereby retract the article. Previous Back to top Next FiguresReferencesRelatedDetailsRelated articlesAngiotensin II–Inducible Smooth Muscle Cell Apoptosis Involves the Angiotensin II Type 2 Receptor, GATA-6 Activation, and FasL-Fas EngagementNicole Y. Tan, et al. Circulation Research. 2009;105:422-430 February 5, 2016Vol 118, Issue 3 Advertisement Article InformationMetrics © 2016 American Heart Association, Inc.https://doi.org/10.1161/RES.0000000000000090PMID: 26846647 Originally publishedFebruary 5, 2016 PDF download Advertisement

Working toward a Paperless Undergraduate Physical Chemistry Teaching Laboratory

The use of electronic formats for obtaining, recording, analyzing, and disseminating data is becoming ubiquitous in classrooms, teaching laboratories, research laboratories, and industry. The undergraduate physical chemistry teaching laboratory provides an excellent opportunity to ensure that upper-division chemistry students gain experience in using electronic means of recording and presenting the results of their experiments. To facilitate this action, computers are used in as many aspects of the course as possible: obtaining introductory material, preparing pre-lab reports, recording data in a simulated electronic lab notebook, and submitting final lab reports. Since the physical chemistry laboratory is an advanced undergraduate course, the students are also given increased responsibility for the experiment, creating their own procedure from papers, textbooks, and other additional information.

Can you hear me now? [Past Forward

From the lab notebook of X., RCA engineer, 1 June 1951: In retrospect, testing ultrahigh-frequency antenna designs by hand with thunderclouds overhead may not have been the best idea. In other news, the company is now seeking qualified applicants to fill four open positions in the ultrahigh-frequency antenna design group. The antennas we're working on will be able to receive a staggering 70 television channels--people will no longer be limited to just 12 VHF channels. We're confident that 82 channels is more than any rational human could ever possibly need.

Wiki Laboratory Notebooks: Supporting Student Learning in Collaborative Inquiry-Based Laboratory Experiments

Recent examples of high-impact teaching practices in the undergraduate chemistry laboratory that include course-based undergraduate research experiences and inquiry-based experiments require new approaches to assessing individual student learning outcomes. Instructors require tools and strategies that can provide them with insight into individual student contributions to collaborative group/teamwork throughout the processes of experimental design, data analysis, display and communication of their outcomes in relation to their research question(s). Traditional assessments in the form of laboratory notebooks or experimental reports provide limited insight into the processes of collaborative inquiry-based activities. A wiki environment offers a collaborative domain that can potentially support collaborative laboratory processes and scientific record keeping. In this study, the effectiveness of the wiki in supporting laboratory learning and assessment has been evaluated through analysis of the content and histories for three consenting, participating groups of students. The conversational framework has been applied to map the relationships between the instructor, tutor, students and laboratory activities. Analytics that have been applied to the wiki platform include: character counts, page views, edits, timelines and the extent and nature of the contribution by each student to the wiki. Student perceptions of both the role and the impact of the wiki on their experiences and processes have also been collected. Evidence has emerged from this study that the wiki environment has enhanced co-construction of understanding of both the experimental process and subsequent communication of outcomes and data. A number of features are identified to support success in the use of the wiki platform for laboratory notebooks.

A Quick Introduction to Version Control with Git and GitHub.

Many scientists write code as part of their research. Just as experiments are logged in laboratory notebooks, it is important to document the code you use for analysis. However, a few key problems can arise when iteratively developing code that make it difficult to document and track which code version was used to create each result. First, you often need to experiment with new ideas, such as adding new features to a script or increasing the speed of a slow step, but you do not want to risk breaking the currently working code. One often-utilized solution is to make a copy of the script before making new edits. However, this can quickly become a problem because it clutters your file system with uninformative filenames, e.g., analysis.sh, analysis_02.sh, analysis_03.sh, etc. It is difficult to remember the differences between the versions of the files and, more importantly, which version you used to produce specific results, especially if you return to the code months later. Second, you will likely share your code with multiple lab mates or collaborators, and they may have suggestions on how to improve it. If you email the code to multiple people, you will have to manually incorporate all the changes each of them sends. Fortunately, software engineers have already developed software to manage these issues: version control. A version control system (VCS) allows you to track the iterative changes you make to your code. Thus, you can experiment with new ideas but always have the option to revert to a specific past version of the code you used to generate particular results. Furthermore, you can record messages as you save each successive version so that you (or anyone else) reviewing the development history of the code is able to understand the rationale for the given edits. It also facilitates collaboration. Using a VCS, your collaborators can make and save changes to the code, and you can automatically incorporate these changes to the main code base. The collaborative aspect is enhanced with the emergence of websites that host version-controlled code. In this quick guide, we introduce you to one VCS, Git (https://git-scm.com), and one online hosting site, GitHub (https://github.com), both of which are currently popular among scientists and programmers in general. More importantly, we hope to convince you that although mastering a given VCS takes time, you can already achieve great benefits by getting started using a few simple commands. Furthermore, not only does using a VCS solve many common problems when writing code, it can also improve the scientific process. By tracking your code development with a VCS and hosting it online, you are performing science that is more transparent, reproducible, and open to collaboration [1,2]. There is no reason this framework needs to be limited only to code; a VCS is well-suited for tracking any plain-text files: manuscripts, electronic lab notebooks, protocols, etc.

A pocket guide to electronic laboratory notebooks in the academic life sciences

Every professional doing active research in the life sciences is required to keep a laboratory notebook. However, while science has changed dramatically over the last centuries, laboratory notebooks have remained essentially unchanged since pre-modern science. We argue that the implementation of electronic laboratory notebooks (eLN) in academic research is overdue, and we provide researchers and their institutions with the background and practical knowledge to select and initiate the implementation of an eLN in their laboratories. In addition, we present data from surveying biomedical researchers and technicians regarding which hypothetical features and functionalities they hope to see implemented in an eLN, and which ones they regard as less important. We also present data on acceptance and satisfaction of those who have recently switched from paper laboratory notebook to an eLN. We thus provide answers to the following questions: What does an electronic laboratory notebook afford a biomedical researcher, what does it require, and how should one go about implementing it?

A pocket guide to electronic laboratory notebooks in the academic life sciences.

Every professional doing active research in the life sciences is required to keep a laboratory notebook. However, while science has changed dramatically over the last centuries, laboratory notebooks have remained essentially unchanged since pre-modern science. We argue that the implementation of electronic laboratory notebooks (eLN) in academic research is overdue, and we provide researchers and their institutions with the background and practical knowledge to select and initiate the implementation of an eLN in their laboratories. In addition, we present data from surveying biomedical researchers and technicians regarding which hypothetical features and functionalities they hope to see implemented in an eLN, and which ones they regard as less important. We also present data on acceptance and satisfaction of those who have recently switched from paper laboratory notebook to an eLN. We thus provide answers to the following questions: What does an electronic laboratory notebook afford a biomedical researcher, what does it require, and how should one go about implementing it?

The CARMEN (Code Analysis Repository and Modelling for E-Neuroscience) project for collaborative sharing of data and analysis tools in electrophysiology: reviewing an early co-laboratory.

The CARMEN (Code Analysis Repository and Modelling for E-Neuroscience) project for collaborative sharing of data and analysis tools in electrophysiology: reviewing an early co-laboratory.

What is the “True” Nature of Diamond?

After having been forgotten for more than half a century, the question of the nature of diamond was again raised by Jean d’ Arcet before the Académie des sciences in the 1770s. Quite surprisingly, diamond totally disappeared when heated to very high temperatures and, in order to understand this fascinating behaviour, Parisian chemists enthusiastically performed experiments from 1771 to 1773. They first used porcelain furnaces and then Tschirnhaus’ lens, an unsurpassed masterpiece constructed in Germany in approximately 1700. The analysis of handwritten laboratory notebooks, describing in detail the experiments conducted with this burning lens, reveals a little known close collaboration between Pierre-Joseph Macquer and Antoine-Laurent de Lavoisier. The successive steps of their research led to the revelation of the “true” nature of diamond, since it burned in air like common charcoal, releasing a gas that precipitated lime water. Contrary to the legend, Trudaine’s lens shed no additional light on the experimental evidence produced by the preceding collaborative academic research.

ChemInform Abstract: Woodward—Hoffmann′s Stereochemistry of Electrocyclic Reactions: From Day 1 to the JACS Receipt Date (May 5, 1964 to November 30, 1964)

AbstractReview: [182 refs.]

Between Provocation and Experiment. Technical Reports and the Ecology of Scholarly Communication in the Humanities

The aim of this paper is to describe a genre that is gaining importance in contemporary humanities, and especially in its areas devoted to digital media – the technical report. Technical reports are discussed as part of the larger trend of open notebook science. This form of communication draws from experiences worked out in the field of technology, computer science and science. In this understanding technical reports are a genre of gray literature, a form dedicated to communicating results of research projects conducted by laboratories. The case study discussed in this text is devoted to a series of technical reports from the MIT Trope Tank lab, which are interpreted in the light of a manifestotext for this form of communication, Beyond the Journal and the Blog. The Technical Report for Communication in the Humanities, published by Nick Montfort. One of the aims of the article is also to contextualize technical reports against the background of other forms and methods of communication in laboratories from the field of contemporary humanities (including blogs, brochures, lab notebooks).

Smart Electronic Laboratory Notebooks for the NIST Research Environment.

Laboratory notebooks have been a staple of scientific research for centuries for organizing and documenting ideas and experiments. Modern laboratories are increasingly reliant on electronic data collection and analysis, so it seems inevitable that the digital revolution should come to the ordinary laboratory notebook. The most important aspect of this transition is to make the shift as comfortable and intuitive as possible, so that the creative process that is the hallmark of scientific investigation and engineering achievement is maintained, and ideally enhanced. The smart electronic laboratory notebooks described in this paper represent a paradigm shift from the old pen and paper style notebooks and provide a host of powerful operational and documentation capabilities in an intuitive format that is available anywhere at any time.

Pypet: a python toolkit for simulations and numerical experiments

(python parameter exploration toolkit [1]) is a new multi-platform python toolkit for management of simulations and storage of numerical data. Exploring or sampling the space of model parameters is one key aspect of simulations and numerical experiments. pypet was especially designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. Moreover, special focus is put on managing different neuron models in python network simulations like BRIAN [2]. Simulation parameters as well as the obtained results are collected by pypet and stored in the widely used HDF5 file format [3]. This allows fast and convenient loading of data for further analyses. Furthermore, pypet provides an environment with various features. For example, among these are multiprocessing for fast parallel simulations, dynamic loading of data, integration of Git version control, and supervision of experiments via the electronic lab notebook Sumatra [4]. A rich set of data formats is supported, encompassing native python types, numpy and scipy data, pandas DataFrames [5], and data from BRIAN [2]. Moreover, the toolkit is easily extendible to allow the user to add customized data formats. pypet is a very flexible tool and suited for short python scripts as well as large scale projects. Thus, pypet supports reproducible research in computational neuroscience and other disciplines that involve simulations and numerical experiments.