Open source data logger for low-cost environmental monitoring
Open source data logger for low-cost environmental monitoring
This 2014 paper by Ed Baker of London’s Natural History Museum outlines a methodology for combining open-source software such as Drupal with open hardware like Arduino to create a real-time environmental monitoring station that is low-power and low-cost. Baker outlines step by step his approach (he calls it a “how to guide”) to creating an open-source environmental data logger that incorporates a digital temperature and humidity sensor. Though he offers no formal conclusions, Baker states: “It is hoped that the publication of this device will encourage biodiversity scientists to collaborate outside of their discipline, whether it be with citizen engineers or professional academics.”
SUSHI: An exquisite recipe for fully documented, reproducible and reusable NGS data analysis
Many next-generation sequencing (NGS) data analysis frameworks exist, from Galaxy to bpipe. However, Hatakeyama et al. at the University of Zürich noted a distinct lack of a framework that 1. offers both web-based and scripting options and 2. "puts an emphasis on having a human-readable and portable file-based representation of the meta-information and associated data." In response, the researchers created SUSHI (Support Users for SHell-script Integration). They conclude that "[i]n one solution, SUSHI provides at the same time fully documented, high level NGS analysis tools to biologists and an easy to administer, reproducible approach for large and complicated NGS data to bioinformaticians."
Laboratory Informatics Weekly Update – Volume 14, Issue 27
July 06, 2016 Laboratory Informatics Weekly Update Volume 14, Issue 27 In This Issue Event Focus July 25-27, 2016: 12th Laboratory Informatics Summit A Comprehensive Discussion on Informatics from Genomics, R&D, Clinical, Quality, and Manufacturing Perspectives to Address Top Industry Challenges! This interactive program will allow for a higher level of discussion on how a more robust informatics structure can lead directly to increased R&D efficiency, faster & more effective clinical trials, reduced downtime in production, and most importantly, more time to focus on innovation when your data is accessed and analyzed with ease. Articles The Benefits of Expert LIMS…Open source data logger for low-cost environmental monitoring
This 2014 paper by Ed Baker of London's Natural History Museum outlines a methodology for combining open-source software such as Drupal with open hardware like Arduino to create a real-time environmental monitoring station that is low-power and low-cost. Baker outlines step by step his approach (he calls it a "how to guide") to creating an open-source environmental data logger that incorporates a digital temperature and humidity sensor. Though he offers no formal conclusions, Baker states: "It is hoped that the publication of this device will encourage biodiversity scientists to collaborate outside of their discipline, whether it be with citizen engineers or professional academics."
Information Competencies for Research Staff
Information Competencies for Research Staff
The LIMSwiki has posted a new
book from the wikibooks collection that we think many research labs will find
useful. The book identifies the skills and knowledge that research
staff should develop to successfully navigate the scientific and chemical
literature as a research chemist.
http://www.limsbook.com/information-competencies-for-research-staff/1920/
The book is published as a free, open access book that can be downloaded as an ebook, read on-line or purchased in printed book form from PediaPress. Please share this book with all research staff that make use of peer reviewed literature and are responsible for publishing peer reviewed papers.
Laboratory Informatics Weekly Update – Volume 14, Issue 26
June 29, 2016 Laboratory Informatics Weekly Update Volume 14, Issue 26 In This Issue Event Focus July 25-27, 2016: 12th Laboratory Informatics Summit A Comprehensive Discussion on Informatics from Genomics, R&D, Clinical, Quality, and Manufacturing Perspectives to Address Top Industry Challenges! This interactive program will allow for a higher level of discussion on how a more robust informatics structure can lead directly to increased R&D efficiency, faster & more effective clinical trials, reduced downtime in production, and most importantly, more time to focus on innovation when your data is accessed and analyzed with ease. The LIMS Book Information Competencies for…The Benefits of Expert LIMS Solution Design
Think back to a time when you first learned to do anything new. Chances are it took longer than expected and the resulting product was less than prize worthy. However, once experience and expertise had been attained, the time it took to accomplish those same tasks had diminished while the quality had markedly improved.Laboratory Informatics Weekly Update – Volume 14, Issue 25
June 22, 2016 Laboratory Informatics Weekly Update Volume 14, Issue 25 In This Issue Webcast Focus Managing your Data - June 23, 2016 - 12:00 PM EDT Any research project requires some level of data management, and with many funding agencies requiring scientists to establish good data management practices, understanding how to manage your lab’s data is critical. To help sort out the numerous choices available, the editors of Lab Manager have assembled a team of industry experts to discuss the latest trends in data management. Join the discussion, ask questions, and learn more in the live webinar presentation. June…Laboratory Informatics Weekly Update – Volume 14, Issue 25
June 22, 2016 Laboratory Informatics Weekly Update Volume 14, Issue 25 In This Issue Webcast Focus Managing your Data - June 23, 2016 - 12:00 PM EDT Any research project requires some level of data management, and with many funding agencies requiring scientists to establish good data management practices, understanding how to manage your lab’s data is critical. To help sort out the numerous choices available, the editors of Lab Manager have assembled a team of industry experts to discuss the latest trends in data management. Join the discussion, ask questions, and learn more in the live webinar presentation. June…Evaluating health information systems using ontologies
Evaluating health information systems/technology is no easy task. Eivazzadeh et al. recognize that, as well as the fact that developing evaluation frameworks presents its own set of challenges. Having looked at several different models, the researchers wished to develop their own evaluation method, one that taps into "evaluation aspects for a set of one or more health information systems — whether similar or heterogeneous — by organizing, unifying, and aggregating the quality attributes extracted from those systems and from an external evaluation framework." As such, the group developed the UVON method, which they conclude can be used " to create ontologies for evaluation" of health information systems as well as "to mix them with elements from other evaluation frameworks."
Laboratory Informatics Weekly Update – Volume 14, Issue 24
June 15, 2016 Laboratory Informatics Weekly Update Volume 14, Issue 24 In This Issue Webcast Focus June 22, 2016, 2:00pm EDT: SAP and LIMS – Living Together (in Harmony) Key considerations when determining your SAP to LIMS integration strategy. Event Focus JUNE 27-29, 2016: High-Content Screening Conference This Conference will gather researchers, academics and industry professionals working in High-Content Screening to explore the latest advances and emerging technologies in the field. Hot topics include novel organisms, novel markers, new essays, novel microscopy techniques, image analysis and statistics. July 25-27, 2016: 12th Laboratory Informatics Summit A Comprehensive Discussion on Informatics from…From the desktop to the grid: Scalable bioinformatics via workflow conversion
This featured article from the journal BMC Bioinformatics falls on the heels of several years of discussion on the topic of reproducibility of a scientific experiment's end results. De la Garza et al. point to workflows and their repeatability as vital cogs in such efforts. "Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization," they state. The researchers developed their own set of free platform-independent tools for designing, executing, and sharing workflows. They conclude: "We are confident that our work presented in this document ... not only provides scientists a way to design and test workflows on their desktop computers, but also enables them to use powerful resources to execute their workflows, thus producing scientific results in a timely manner."
