Lurking in the Lab: Analysis of Data on Molecular Biology Laboratory Instruments

OBJECTIVE Experimental data files found on molecular biology laboratory instruments were examined in order to: (1) gain insight into current data management practices, and (2) evaluate possible curation and preservation challenges with this type of data. METHODS A faculty member granted me access to several instruments in her molecular biology teaching lab. Files and metadata on the hard drives were captured using Xplorer2 file management software. Data file formats were sorted and analyzed with Xplorer2 and Microsoft Excel, and formats were categorized as proprietary or open. Informal discussions with the faculty member and research staff during the course of the work also informed the findings. RESULTS Files in both proprietary and open formats were found on the instruments\u27 hard drives. 62% of the experimental data files were in proprietary formats. Image files in various formats accounted for the most prevalent types of data found. Faculty and research staff mentioned several challenges in managing this data, including inconsistent practices in data storage locations and file naming conventions. They noted that students found working with and sharing experimental data frustrating at times, largely due to proprietary format issues. CONCLUSIONS This study found lack of a consistent approach to data management on laboratory instruments. Prevalence of proprietary file formats is a concern with this type of data. Students express frustration in working with this data now, and files in these proprietary formats may well pose curation and preservation challenges in the future

Description and annotation of biomedical experimental data sets: work in progress

OBJECTIVE: Collaborating with researchers and curators from The Harvard School of Public Health Bioinformatics Core (HSPH/HBC) to annotate experimental descriptions and data sets. METHODS: ISATab is an open source software suite that can be used to annotate and apply metadata to experimental data. HSPH/HBC curators create ISATab records tying together information from PubMed papers and associated data sets (GEO files). Curators annotate and describe both raw and derived data files for each investigation, as well as supplying metadata for the investigation as a whole. Once annotated, the records are validated and sent to an internal data management system. RESULTS: As of Jan. ’11, HBC has collected over 50 annotated public studies comprising 900+ assays in their internal data management system. The ultimate goal is to make curated, metadata-enriched data sets openly available in public repositories, allowing for further data analysis & integration. CONCLUSIONS: Researchers & curators in this group grapple with many of the same issues around data curation and discovery that librarians do. For example, how much metadata is adequate to ensure discovery, and where’s the sweet spot between too much and too little? Where are ontologies necessary? Do all experiments comprising a published work need to be described, or just a selection? My experiences working as a curator with HSPH/HBC have given me some good insights into how librarians can be involved in e‐science in ways that can benefit all concerned

Description and Annotation of Biomedical Data Sets

Deposition of biomedical data sets is on the rise as more scientists submit experimental data to accompany their publications. Scientists are also increasingly reusing these publicly available data sets in their own work. Despite these developments, lack of both context and metadata can create barriers to understanding and repurposing these data sets. Researchers from the Bioinformatics Core Group in the Harvard School of Public Health attempted to address this issue by assembling a team of data curators who used the open source software suite ISA tools to annotate and contextualize microarray data sets. This paper describes the workflow and software used in curating these data sets, discusses similarities and differences in the approaches of team members to the work, and suggests possible roles for librarians in similar data curation projects

What are they saying about us? References to library support & services in grant proposals

This presentation discussed a project at Northeastern University to review NSF and NIH grant proposals for references to library services and support. Presented at the National Network of Libraries of Medicine New England Region e-Science Forum, Marlborough, MA, USA, on March 29, 2019

Lurking in the Lab: Analysis of Data from Molecular Biology Laboratory Instruments

OBJECTIVE: This project examined primary research data files found on instruments in a molecular biology teaching laboratory. Experimental data files were analyzed in order to learn more about the types of data generated by these instruments (e.g. file formats), and to evaluate current laboratory data management practices. SETTING: This project examined experimental data files from instruments in a teaching laboratory at Brandeis University. METHODOLOGY: Experimental data files and associated metadata on instrument hard drives were captured and analyzed using Xplorer2 software. Formats were categorized as proprietary or open, and characteristics such as file naming conventions were noted. Discussions with the faculty member and lab staff guided the project scope and informed the findings. RESULTS: Files in both proprietary and open formats were found on the instrument hard drives. 62% of the experimental data files were in proprietary formats. Image files in various formats accounted for the most prevalent types of data found. Instrument users varied widely in their approaches to data management tasks such as file naming conventions. CONCLUSIONS: This study found inconsistent approaches to managing data on laboratory instruments. Prevalence of proprietary file formats is a concern with this type of data. Students express frustration in working with these data, and files in these proprietary formats could pose curation and preservation challenges in the future. Teaching labs afford an opportunity for librarians interested in learning more about primary research data and data management practices

Do funding agency data policies conflict with text mining license terms?

Objective: As text/data mining (TDM) becomes more prevalent, researchers seek to mine library resources for their projects. Some vendors are including language in their TDM licenses that aims to protect their investments by limiting dissemination and/or retention of TDM data. At the same time, researchers are increasingly being called upon by funding agencies to share and retain data from their projects. This work investigated whether vendor restrictions on TDM data sets from research projects might conflict with funder policies on data sharing and retention. Methods: Language from existing TDM licenses was compared with guidance from several grant-funding agencies to identify potential conflicts with sharing or retaining data generated in the course of TDM research projects. Results: Potential incompatibilities between TDM licensing language and funding agency data policies were identified. Vendor limitations on the length of TDM output could conflict with data sharing policies. Data retention is an area of particular concern, as in some cases, funder policies on data retention periods are at odds with TDM licensing terms that require data to be destroyed upon conclusion of the work. Conclusions: In some cases, language in library vendor TDM licenses is at odds with funding agency policies on data sharing and retention. As support for TDM research continues to evolve, librarians who assist researchers with data management plans should be aware of potential conflicts between vendor TDM licenses and funder data policies on data sharing and preservation

The Usage of Indigenous Languages as a Tool for Meaningful Engagement With Northern Indigenous Governments and Communities

The Canadian Northern Corridor (CNC) program integrates formal academic research and a strategy of engagement with potentially impacted communities (Fellows et al. 2020). Finding common ground among Indigenous peoples, governments and industry on engagement and consultation practices is imperative to the future of resource development and the Canadian economy, and ultimately to the reconciliation of the relationships between Indigenous Peoples and Canada (Boyd and Lorefice 2018). In this paper, we focus on language, stressing that languages are more than just tools. Rather, all communicative systems also hold both individual and cultural identities, histories and memory, and encode knowledge in specific ways. This article investigates how Indigenous languages can contribute to meaningful engagement particularly within the context of the CNC concept; our recommendations also work toward strengthening existing Indigenous policy initiatives in Canada, uplifting Indigenous worldviews, and potentially supporting the reconciliation process. We draw upon primarily Indigenous scholars in explaining the reasons why using Indigenous languages matters for fostering meaningful engagement during research, consultation, and community engagement activities and address methods by which they can be implemented. After examining some past/ongoing attempts at this incorporation, we identify in our policy recommendations five different ways that the entire process of community engagement can align with the usage of Indigenous languages

Lost in Translation

The meaningful incorporation of Traditional Ecological Knowledge (TEK) into large-scale northern infrastructure construction can improve sustainability practises and broaden our conceptual understanding of nature (Sidorova and Virla 2022). TEK refers to systems of collective knowledge production, established gradually by members of Indigenous and local communities and transferred through generations (Agrawala et al. 2010). While the ‘traditional’ part of the term TEK can be problematic, as the word may connote something old and static, we stress here that TEK is a dynamic, living tradition adaptable to new conditions and knowledge. Another key element in infrastructure projects is the Environmental Impact Assessment (EIA). EIAs are used to evaluate the likelihood of negative environmental impacts before deciding whether to move forward with a project. They also attempt to develop and implement strategies to avoid or reduce those negative impacts as conditions of approval for the project (Agrawala et al. 2010). This paper examines a particular tension that arises between TEK and EIA

Exercise trained postmenopausal women have higher arterial stiffness than men before and after an acute bout of dynamic exercise

Objectives Arterial stiffness, peripheral wave reflection and pulse pressure predict cardiovascular disease risk. Regular aerobic exercise training is a recommended non-pharmacological approach to lower cardiovascular disease risk, including lowering blood pressure and attenuating age-related increases in arterial stiffness (AS). However, it remains unclear whether sex differences differentially modulate vascular adaptations to exercise training and/or influence vascular compliance. Thus, we sought to examine the independent and combined effects of aerobic conditioning and an acute bout of dynamic exercise, a known nitric oxide stimulus, on AS in healthy middle-aged men and postmenopausal women (PMW).Methods Two age-matched (54±1 years; mean±SEM) groups of habitually aerobically trained men (n=6; VO2peak 49.8±1.2 ml/kg/min) and postmenopausal women (n=6; VO2peak 38.5±1.4 ml/kg/min) were studied. Pulse wave analysis using applanation tonometry methods was used to assess arterial stiffness (augmentation pressure [AP; mmHg] and augmentation index corrected for heart rate [AIx75;%]). Central measures of blood pressure (systolic BP, SBP; diastolic BP, DBP; pulse pressure, PP; mmHg) were determined using a validated transfer function. AS and BP were recorded at baseline and 60 min after an acute bout of moderate intensity exercise (45 min of brisk walking at 60% VO2peak).Results Our preliminary findings (see table 1) demonstrate that baseline AP and AIx75 were higher, (p0.05) for baseline measures of central BP but brachial SBP and PP were lower (pConclusions Our preliminary findings suggest that compared with habitually aerobically trained PMW, trained men demonstrate lower peripheral wave reflection yet higher PP amplification both before and after an acute bout of exercise. Associations between PP and AIx75 were observed in men but not women. While the clinical significance of these findings cannot be determined, these observations suggest: i) arterial stiffness is lower in aerobically trained men versus women, and ii) the relationship between PP and arterial stiffness may differ between men and women. Such differences may be of relevance to the known sex differences in the development and progression of hypertension with ageing.</div

Lost in Translation

The meaningful incorporation of Traditional Ecological Knowledge (TEK) into large-scale northern infrastructure construction can improve sustainability practises and broaden our conceptual understanding of nature (Sidorova and Virla 2022). TEK refers to systems of collective knowledge production, established gradually by members of Indigenous and local communities and transferred through generations (Agrawala et al. 2010). While the ‘traditional’ part of the term TEK can be problematic, as the word may connote something old and static, we stress here that TEK is a dynamic, living tradition adaptable to new conditions and knowledge. Another key element in infrastructure projects is the Environmental Impact Assessment (EIA). EIAs are used to evaluate the likelihood of negative environmental impacts before deciding whether to move forward with a project. They also attempt to develop and implement strategies to avoid or reduce those negative impacts as conditions of approval for the project (Agrawala et al. 2010). This paper examines a particular tension that arises between TEK and EIA