Archive for the ‘E-Science’ Category
NCBI will present the first iteration of NCBI NOW, a free online experience aimed at those new to next generation sequencing (NGS) analysis, from October 13-23. Enrollment in this course is limited to the first 1,000 participants who sign up through the ORAU Portal. Since enrollment is on a first-come, first-served basis, please only sign up for this educational opportunity if you will be able to participate fully. Learners will watch 6-7 videos (average video duration: 45-60 minutes) online during the first seven days of the course. These videos will cover the basics of NGS data, preprocessing, quality control and alignment strategies for both DNA-Seq and RNA-Seq, as well as a brief discussion of downstream analysis. Additionally, there will be demonstrations about leveraging BLAST tools for NGS analysis.
Next, participants will apply a selection of RNA-Seq alignment algorithms over three days (1-2 hours per day), mapping RNA-Seq data to GRCh38 chromosome 20. Finally, participants will compare the results of these mappers for specific genes. Throughout the course, participants will be able to post questions at Biostars; experts from NCBI and elsewhere will be available online to answer questions. Learners will emerge from the course equipped to map their own RNA-Seq or DNA-Seq data to the human genome, understand the options for downstream analysis, and use their understanding of the basic steps of data processing to interact more effectively with bioinformatician collaborators.
The National Library of Medicine is pleased to announce the first annual Donald A.B. Lindberg & Donald West King Lecture on Wednesday, October 7, at 10:00 AM PDT in Bethesda, MD, and will be videocast (and archived for later viewing). The inaugural lecture, which honors recently retired NLM Director Dr. Lindberg and former NLM Deputy Director of Research and Education Dr. King, is titled, Integrating Multi-scale Data for Biomedical Discovery and Clinical Implementation. It will be given by Russell Altman, MD, PhD, of Stanford University. Dr. Altman’s primary interests are in the field of bioinformatics. He is particularly interested in the analysis of protein and RNA structure and function, both in an individual problem-centered manner and on a functional genomic scale. Dr. Altman currently serves as a member of the Advisory Committee to the NIH Director (ACD).
NIH encourages the use of common data elements (CDEs) in clinical research, patient registries, and other human subject research in order to improve data quality and opportunities for comparison and combination of data from multiple studies and with electronic health records. The NIH Common Data Element Resource Portal provides access to information about NIH-supported CDEs, as well as tools and resources to assist investigators developing protocols for data collection. In addition, the session recording and presentation slides for the 90-minute webinar “NIH Common Data Element (CDE) Initiatives – Overview,” held on September 8, are available for viewing.
Data management activities present opportunities for librarians to adopt new roles and support the research process in their institutions. There is a variety of educational resources available to librarians wishing to get started in this field and learn more about data management and related functions. One example is MANTRA: Research Data Management Training, an online course sponsored by the University of Edinburgh, which is freely available to anyone to explore. It consists of nine online units, such as “Organising Data,” Storage & Security,” and “Sharing, Preservation, & Licensing.” Each unit takes up to one hour to complete, plus time for further reading and data handling exercises. The current course content represents the fourth release of MANTRA in September, 2014. Data Management for Clinical Research is a five-week free online course offered by Coursera. It utilizes best-practice guidelines, along with hands-on demonstrations and exercises, to cover important concepts related to research data collection and management, with a primary focus on data management for patient-centered research. The Medical Library Association also offers continuing education opportunities related to data management.
In addition to these courses, a Mendeley group, Data Management for Librarians, is an active community created for librarians of all disciplines to share literature and resources about data management and related areas. Members are also encouraged to share their experiences working with data in their institutions. Another introductory resource is the article “Research Data Management,” by Alisa Surkis, PhD, MLS; and Kevin Read, MLIS, MAS; both of NYU Health Sciences Library, published in the July 2015 issue of the Journal of the Medical Library Association.
The NN/LM New England Region has announced the launch of the newly redesigned e-Science Portal for New England Librarians. Along with a new look, features of the e-Science Portal 2.0 include:
- A “Getting started with e-Science” quick guide
- Events calendar and Twitter feed
- Links to recent e-Science Community blog posts
- Prominent hyperlinks to e-Science Partner Projects (New England e-Science Symposium, Science Boot Camp, New England Collaborative Data Management Curriculum (NECDMC), Journal of eScience Librarianship)
- Reorganized content headings (e.g. About, Connect with Others, Data Management, and Research Environment sections)
- Links to data tools posted on a delegated “Data Tools” page as well as in relevant pages such as data curation
- Editor’s photo, biography, and contact form on portal pages
For further details about the portal redesign, visit the e-Science Community blog post Portal 2.0 is here, by Jen Ferguson, co-chair of the e-Science Portal Editorial Board.
The NIH Big Data to Knowledge (BD2K) program and the NIH Library are pleased to join the Johns Hopkins (JHU) Bloomberg School of Public Health Department of Biostatistics in announcing the first JHU DaSH, Data Science Hackathon, on September 21-23, 2015, in Baltimore.
The event organizers, Drs. Brian Caffo, Leah Jager, Jeff Leek and Roger Peng, include JHU professors who teach the popular Coursera Data Science Specialization. This Data Science Hackathon will provide an opportunity for hands-on training that reinforces and builds on data management and analysis skills, and provides a local opportunity for NIH scientists and trainees to participate in a data science Hackathon. For questions about the Hackathon, contact Lisa Federer at the NIH Library.
A new Big Data to Knowledge (BD2K) funding opportunity (FOA) is available, Development of Software Tools and Methods for Biomedical Big Data in Targeted Areas of High Need, with an October 6 application due date. This FOA solicits development of innovative analytical methods and software tools with the objective of addressing critical current and emerging needs of the biomedical research community for using, managing, and analyzing the larger and more complex data sets inherent to biomedical big data, focusing on the three topic areas of Data Privacy, Data Repurposing, and Applying Metadata, all as part of the overall BD2K initiative. This FOA aims to support the development of innovative tools and approaches to tough problems, as opposed to having fully fledged software tools developed for less-daunting problems. It is not expected that software and methods developed under this FOA will be fully hardened, but rather that investigators show a novel approach to a difficult problem and show some proof-of-concept for this new approach using relevant biomedical big data. While this FOA is intended to foster new development, submissions consisting of significant adaptations of existing methods and software are also invited.
It is anticipated that a single application will have a primary focus on one of the three topic areas. Applicants can submit multiple independent applications, each addressing a separate topic area. The award mechanism will be a Cooperative Agreement, used used when there will be substantial Federal scientific or programmatic involvement. Substantial involvement means that, after the award, NIH scientific or program staff will assist, guide, coordinate, or participate in project activities. NIH intends to fund 8-12 awards in fiscal year 2016, corresponding to a total of $5 million. The maximum project period is three years, and direct costs are limited to a maximum of $300,000 in each year. Scientific Merit Reviews of applications are expected in February 2016, and the earliest award start date is expected in July, 2016.
NLM is announcing on behalf of the IHTSDO (International Health Terminology Standards Development Organization) the formation of seven new IHTSDO Advisory Groups (AGs). The AGs are the successors of the IHTSDO Standing Committees, which will allow for a more agile and flexible structure. The AGs will conduct specific activities that will contribute to the fulfillment of the IHTSDO Management Team’s responsibilities or the organization’s mandate.
The IHTSDO is seeking volunteers to serve on the following AGs:
- Content Managers Advisory Group
- E-Learning Advisory Group
- Modeling Advisory Group
- SNOMED CT Editorial Advisory Group
- Software Developers Advisory Group
- Terminology Release Advisory Group
- Tooling User Advisory Group
For additional information on the different Advisory Groups as well as the nomination and application process, please see the IHTSDO news note, Join an Advisory Group. The nomination period is open until August 14, 2015.
The National Library of Medicine’s ChemIDplus Lite and ChemIDplus Advanced interfaces have been enhanced with the following features:
- Valid chemical names and CAS RN completions are displayed as the user types in the search box. If no data are found, suggestions are provided.
- The ChemIDplus Registry Number field now includes the FDA UNII code.
- The InChIKey is now directly searchable. It can be used for the interchange of structural data and as input for search engines such as Google.
- The ChemIDplus Formula field now accepts molecular formulas with spaces between elements and their counts and without the hyphens previously required.
Examples of these new features may be viewed at the ChemIDplus Help pages. ChemIDplus is a free, web search system that provides access to the structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases, including the TOXNET® system. ChemIDplus also has structure searching and direct links to resources at NLM, federal agencies, U.S states, and scientific sites. The database contains more than 400,000 chemical records, of which over 300,000 include chemical structures.
Have you ever wanted to be able to use mapping for your outreach needs, but thought that making maps would be too expensive, time-consuming, or just too difficult? The main goal of the National Library of Medicine’s Community Health Maps: Information on Low Cost Mapping Tools for Community-based Organizations blog is facilitating the use of geographic information system (GIS) mapping by providing information about low cost mapping tools, software reviews, best practices, and the experiences of those who have successfully implemented a mapping workflow as part of their work. The blog is moderated by Kurt Menke, a certified GIS professional.
Here are some examples of the kinds of things you can find on the Community Health Maps blog:
- A short guide for using iForm for field data collection. iForm is an app that can be used on iPads, iPhones and Android devices, and has a free version. Using this app, you can go to different locations, gather data (for example, demographic information about attendance at your program), and view it in tabular or map format.
- A description of a project using youth in the Philippines to collect data on the needs of their communities. Technology + Youth = Change showed how a dozen donated phones helped 30 young adults survey and map information on access to water, electricity, jobs, and more.
- A review of a pilot project done by the Seattle Indian Health Board’s Urban Indian Health Institute on noise pollution and health in the urban environment.