Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid achievement in cancer diagnosis and therapeutics.

A high efficiency, high quality and low cost internal regulated bioanalytical laboratory to support drug development needs.

In the recent past, we have seen an increase in the outsourcing of bioanalysis in pharmaceutical companies in support of their drug development pipeline. This trend is largely driven by the effort to reduce internal cost, especially in support of late-stage pipeline assets where established bioanalytical assays are used to analyze a large volume of samples. This article will highlight our perspective of how bioanalytical laboratories within pharmaceutical companies can be developed into the best partner in the advancement of drug development pipelines with high-quality support at competitive cost.

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.

Quality assurance mechanisms for the unregulated research environment.

Discussions on research quality and reproducibility are appearing in the pages of scientific journals with heightened significance and gaining media attention. Many institutions have developed guidelines to address the topic of quality in basic research, but questions remain about how best to implement and monitor compliance. Herein we present quality assurance (QA) mechanisms developed specifically for the unregulated discovery research environment to preempt growing concerns arising in both academia and industry for data-driven applications of biotechnology.

Using Evernote as an electronic lab notebook in a translational science laboratory.

Electronic laboratory notebooks (ELNs) offer significant advantages over traditional paper laboratory notebooks (PLNs), yet most research labs today continue to use paper documentation. While biopharmaceutical companies represent the largest portion of ELN users, government and academic labs trail far behind in their usage. Our lab, a translational science laboratory at New York University School of Medicine (NYUSoM), wanted to determine if an ELN could effectively replace PLNs in an academic research setting. Over 6 months, we used the program Evernote to record all routine experimental information. We also surveyed students working in research laboratories at NYUSoM on the relative advantages and limitations of ELNs and PLNs and discovered that electronic and paper notebook users alike reported the inability to freehand into a notebook as a limitation when using electronic methods. Using Evernote, we found that the numerous advantages of ELNs greatly outweighed the inability to freehand directly into a notebook. We also used imported snapshots and drawing program add-ons to obviate the need for freehanding. Thus, we found that using Evernote as an ELN not only effectively replaces PLNs in an academic research setting but also provides users with a wealth of other advantages over traditional paper notebooks.