Laboratory Notebooks Research Articles

Use of a Wiki-Based Software to Manage Research Group Activities.

This paper discusses use of the wiki software Confluence to organize research group activities and lab resources. Confluence can serve as an electronic lab notebook (ELN), as well as an information management and collaboration tool. The article provides a case study in how researchers can use wiki software in "home-grown" fashion to organize their research activities and how librarians can play a role in exploring or advocating wiki software for these purposes. Most of the focus in our discussion will be on ELNs, but we will also address other uses of Confluence. [ABSTRACT FROM AUTHOR]

연구노트 도입의 필요성과 전자연구노트

연구과정과 성과를 기록으로 보존하는 것은 연구자의 중요한 의무이자 덕목이다. 이는 연구의 객관성과 진실성을 뒷받침해주며, 후학들의 연구에 중요한 초석이 되기도 한다. 나아가 연구의 중복을 피할 수 있게 됨으로써 자원과 시간을 절약할 수도 있다. 최근에는 특허 출원과 관련하여 연구노트의 가치는 증가되고 있다. 하지만, 방대한 자료를 가지는 연구결과를 기록하기에는 서면연구노트는 한계가 있다. 이에 대한 대안은 서면연구노트를 전자문서화 하거나 전자연구노트를 각 분야의 특성에 맞게 개발하는 것이다. 우리 학회지는 지속적으로 국제화를 추구해 왔다. 학회지의 평가 항목 중에서 연구노트의 활용은 중요한 요소이다. 이에 본 저자들은 사용의 편의성과 개발 및 유지비용 등을 고려한 proto-type의 전자연구노트 시스템을 개발해보고자 하였다. Recording of the research procedure and results is the compulsory virtue to scientists. This ensures the objectivity and integrity of research and has become a cornerstone for a junior scholar. Furthermore, we can save time and efforts by avoiding duplication study. Recently on its patent application, the value of laboratory notebook is going to increase. However, there is a limitation to record a voluminous work in a traditional writing laboratory notebook. So, it could be an alternative proposal to convert that into an electronic work or develop an electronic laboratory notebook. Our journal has continuously pursued globalization. Laboratory notebook could be one of the key factors for that goal. In the present study, the authors reviewed the needs for laboratory notebook and tried developing a proto-type electronic laboratory notebook.

Opening up the Lab Notebook: Publishing Experimental & Supplementary Information

Supplementary Information supporting publications is not uniform across journals, is generally not 100% representative of the work undertaken, is not structured or comprehensive and therefore is often not fully considered in review. In chemistry articles where characterisation techniques are applied widely, crystallography is the exception in that there are universally agreed processes and protocols for presenting the scientific findings and the supporting data. Crystallography can therefore lead the way! Our approach to solving the broader problem of availability of supporting information is to expose the observations of the researchers who conducted the work when it was performed. By combining these observations with related data (eg in information management systems) and linking these with the article there is the potential for a much richer system for data supporting a publication. The Electronic Laboratory Notebook (ELN) plays a key role by establishing authenticity, adding structure to the record and having the capacity to be made open. We present a formal publication in Chemistry Central Journal (http://journal.chemistrycentral.com/content/7/1/182) which is a collaborative piece of work between the UK National Crystallography Service (University of Southampton) and the University of Greenwich, where the data supporting the article is not contained within it, but is openly exposed at source by an ELN and a crystal structure repository. We draw on the experience of crystallographic publishing and aligning that with the other characterisation techniques alongside which crystal structures are routinely published and related. The article presents all the supplementary information (some 35 or so data sources) in a single graphical approach, which permits examination of synthesis, spectra & structures in-line and provides a link to the original ELN record. All records are assigned a Digital Object Identifier (DOI) by a system established within the University.

Delivering practical crystallography experience to undergraduate students

Teaching of laboratory-based chemistry in universities has barely evolved since its inception. Practical work is generally conducted in a highly structured, dedicated teaching laboratory environment or on a `student-as-apprentice' basis in an active research laboratory. Exposure to crystallography as an undergraduate is generally limited to theoretical lecture-based courses, with little or no practical experience, despite the fact that training in the use of expensive research-based instruments is becoming a necessity of modern science. We present a course based around the solid-state structural chemistry of a molecular polymorphic system, delivered to third year undergraduates (70 students) at the University of Southampton which contains numerous novel features: 1) Students work in pairs (maximum group size of 8). 2) It is a `hands-on' experience for every participant, involving single crystal and powder diffractometers (Rigaku XtaLab mini and MiniFlex benchtop systems) dedicated to educational activities. 3) It is a student-led activity, designed as an `advanced practical' providing a taste of the research experience. 4) Laboratory manuals are available to students via an Electronic Laboratory Notebook (ELN) system. 5) Plans, experimental enactments, observations and conclusions are recorded by students in the ELN (directly linked to the manual sections). 6) Feedback and assessment is delivered through the ELN by directly linking instructor comments to the student ELN record. The experiment comprises about 15 manual sections in the LabTrove ELN system, which has a similar design to a blog, enabling student comments and assessor feedback to be linked to these sections. This talk will outline the design of the experiment and instruments involved, the mode and logistics of delivery, and will discuss the evaluation of its impact on student learning by analysis of feedback questionnaires.

LIFE SCIENCE TECHNOLOGIES: DIGITAL LAB MANAGEMENT

Some scientists keep experimental records on sticky notes. Some groups maintain ordering information in the head of a single technician. But for researchers looking for more stable, searchable, and sharable records, digital options such as electronic laboratory notebooks (ELNs) and laboratory information management systems (LIMS) are readily available. Scientists can start with a simple online notebook or choose a complete lab management package to track the entire lifecycle of their projects.

Mel - personal reminiscence.

Mel - personal reminiscence.

Electronic Lab Notebooks: Supporting Laboratory Data in the Digital Era.

This article focuses on the collaboration of Yale University Library (YUL) and Information Technology Services (ITS) to introduce a service providing institutional support for electronic lab notebooks (ELN). Topics discussed the process involved in choosing a product, support considerations and the alternative steps that the groups might have taken. The outcome of the effort are explored.

(2014 Mellor Lecture) Experiences with LabTrove, a researcher-centric electronic laboratory notebook ELN: undergraduate possibilities and Twitter.

(2014 Mellor Lecture) Experiences with LabTrove, a researcher-centric electronic laboratory notebook ELN: undergraduate possibilities and Twitter.

Forgotten fluids of the reproductive tract

Forgotten fluids of the reproductive tract

The laboratory notebook in the 21st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity.

Detailed note‐keeping is a prerequisite for, if not a key component of, scientific discovery. An unrecorded experiment is lost to the world even if it sparks a great idea in a scientist's mind: Additional work is needed to reproduce and confirm the original observation and to test the hypothesis by novel experimental strategies. Hence, a detailed record of the experimental setup, observations, and analysis is a crucial requirement for presenting a new discovery to the scientific community. > An unrecorded experiment is lost to the world even if it sparks a great idea in a scientist's mind… For centuries, scientists have been using paper notebooks. However, the digital revolution has changed every aspect of data handling: Acquisition has become automated, primary data exist in a huge variety of formats and require vast memory space, and analysis increasingly uses sophisticated software. While electronic note‐keeping has become state of the art in the pharmaceutical industry, it is by far not the standard in academic life‐science laboratories. In fact, digital record‐keeping has been controversial in academia, and hence, its implementation has been lagging. We argue that many academic laboratories will soon abolish the current precarious mixture of digital data and paper‐based annotation. We see three main reasons for this trend. First, the vast majority of the data generated by a scientist will be in digital form that has to be documented and archived; however, the paper‐based laboratory notebook does not enable convenient documentation of folder structures and data paths. Second, ongoing efforts aim to standardize experimental protocols and data formats in order to improve their general comparability and re‐analysis of data, which make standardization more attractive for scientists. In fact, standardization is a prerequisite for using an electronic laboratory notebook (ELN). Third, long‐term data storage, an essential component of good scientific practice, easily turns …

An Almost Paperless Organic Chemistry Course with the Use of iPads

The advancement of tablet computer technology has progressed rapidly in the past three years to the point where organic chemistry can be almost completely paperless. Students in one section of organic chemistry were provided iPads equipped with the application Notability to use in lecture to take notes and to use in the laboratory as a laboratory notebook. All laboratory assignments were completed, submitted, graded, and returned to the students electronically. Student feedback about using iPads in class was very positive, with 9-out-of-12 students preferring to use an iPad to take notes rather than the traditional paper and pencil method.

Research tools: Jump off the page

Researchers are learning to embrace online lab notebooks, but not without growing pains.

Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices.

The presentation will describe 4 years of work creating chemical structure based user interfaces for mobile devices, combined with creation of cloud-hosted webservices for supporting functionality. A number of products have been created along the way, for drawing structures and reactions, managing collections of data, searching databases, creating publication quality graphics, sharing and collaborating, calculating properties, and model building for drug discovery research. The focus will be on the assembly of these core technologies to create a fully featured electronic lab notebook (ELN) product for capturing chemical reactions. While a number of web or mobile products already exist for laboratory notetaking, none of them provide the high level chemistry understanding and sophisticated cheminformatics functionality that will be described. The ability to combine all of the necessary capabilities onto a mobile device such as an iPhone or iPad demonstrates that this new generation of computing platforms is ready to play an important role in the realm of cheminformatics.

Online repository for lab notebooks

Online repository for lab notebooks

Closing the feedback loop: physics undergraduates’ use of feedback comments on laboratory coursework

The laboratory notebooks of physics undergraduates taking two second-year practical courses were audited to discover whether they had used feedback comments in their subsequent coursework. Ninety-five per cent of the 37 students on the first course and 100% of the 14 students on the second course whose work was audited had used feedback. The marker’s comments were classified into two groups based on whether they addressed simple (mastery) or complex (developmental) learning outcomes. Mastery comments were more likely to be acted on than developmental comments which aimed to extend students’ skills and understanding to higher levels. This has implications for the use of feedback audit as a quality control process, since the feedback which is most commonly applied by students is not the most valuable for the development of higher order skills. Following reflection on the results for the first course, students taking the second course were given responsibility for checking their peers’ notebooks against preset criteria. Peer checking improved students’ marks but did not eliminate the need for mastery feedback. It is argued that a direct audit of students’ use of feedback is particularly valuable when undertaken by the teacher who provides the feedback.

Mobile metadata: bringing Neuroinformatics tools to the bench

Mobile metadata: bringing Neuroinformatics tools to the bench

Developing A Strategy for A Regulated Electronic Bioanalytical Laboratory

This perspective article considers the strategy, design and implementation of an electronic bioanalytical laboratory working to GLP and/or GCP regulations. There are a range of available automated systems and laboratory informatics that could be implemented and integrated to make an electronic laboratory. However, which are the appropriate ones to select and what is realistic and cost-effective for an individual laboratory? The answer is to develop an overall automation strategy that is updated periodically after each system or application has been implemented to assess if the strategy is still valid or needs to be changed. As many laboratory informatics applications have functional overlap or convergence, for example, Laboratory Information Management System, Electronic Laboratory Notebook, and Instrument and Chromatography Data Systems, the decision of which application performs a specific task needs to be carefully considered in the overall strategy. Ensuring data integrity and regulatory compliance, especially in light of a number of recent falsification cases, is a mandatory consideration for the overall strategy for an electronic bioanalytical laboratory submitting data to regulatory authorities.

Integrating standard operating procedures and industry notebook standards to evaluate students in laboratory courses

To enhance the preparedness of graduates from the Biochemistry and Biotechnology (BCBT) Major at Minnesota State University Moorhead for employment in the bioscience industry we have developed a new Industry certificate program. The BCBT Industry Certificate was developed to address specific skill sets that local, regional, and national industry experts identified as lacking in new B.S. and B.A. biochemistry graduates. The industry certificate addresses concerns related to working in a regulated industry such as Good Laboratory Practices, Good Manufacturing Practices, and working in a Quality System. In this article we specifically describe how we developed a validation course that uses Standard Operating Procedures to describe grading policy and laboratory notebook requirements in an effort to better prepare students to transition into industry careers.

Using an ePortfolio system as an electronic laboratory notebook in undergraduate biochemistry and molecular biology practical classes

Despite many apparent advantages, including security, back-up, remote access, workflow, and data management, the use of electronic laboratory notebooks (ELNs) in the modern research laboratory is still developing. This presents a challenge to instructors who want to give undergraduate students an introduction to the kinds of data curation and notebook keeping skills that will inevitably be required as ELNs penetrate normal laboratory practice. An additional problem for the teacher is that ELNs do not generally have student-administrative functions and are prohibitively expensive. In this report, we describe the use and impact of an ePortfolio system as a surrogate ELN. Introduction of the system led to several pedagogic outcomes, namely: increased preparedness of students for class, encouragement of creativity and reflection with respect to experimental methods, greatly enhanced engagement between students and tutors, and it gave instructors the ability to scrutinize original data files and monitor student-tutor feedback cycles. However, implementation led to a disruption of tutor workloads and incurred new levels of accountability that threatened to undermine the initiative. Through course evaluations and other reflective processes, we reached an appreciation of how an ELN should be introduced into practical class teaching so that it not only becomes an appropriate aid for teaching the laboratory experience, but also becomes a life-long resource for students.

Molecule database framework: a framework for creating database applications with chemical structure search capability

BackgroundResearch in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time.ResultsMolecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:• Support for multi-component compounds (mixtures)• Import and export of SD-files• Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.ConclusionsBy using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.