TOXinvaders supports middle school science concepts pertaining to chemistry, the environment, and health. It can serve as an engaging classroom or homework activity for middle and high school students, as well as an entertaining learning activity for gaming aficionados of all ages. In the classroom environment, TOXinvaders works best as a supplement to NLM Tox Town, Environmental Health Student Portal, TOXMAP, and ChemIDplus Web sites.
The game consists of four fast-paced levels, in which a launcher is used to annihilate toxic chemicals falling from the sky and earn protective shield points by capturing “good chemicals.” To move on to the next level, players must take a brief quiz about the chemicals. These dynamically generated tests provide an excellent opportunity to learn more about environmental health and toxicology from the game’s chemical information sheet and from NLM Web sites. Quiz questions and answers can also serve as a starting point for classroom discussions, as well as for Tox Town, TOXMAP, and Environmental Health Student Portal activities and experiments.
The Next Generation of Access to Sequencing Data: Using NCBI’s SRA Toolkit to Access Data from dbGaP and SRA
Next Wednesday, February 25, NCBI staff will present a webinar on the SRA Toolkit (Sequence Read Archive), a system for accessing the approximately 3.4 Petabases of next-generation genomic and expressed sequence data housed in the NCBI Sequence Read Archive (SRA). As data sets become larger, mining information and performing comparisons directly from structured databases becomes increasingly necessary. The SRA Toolkit is not only capable of dumping the data out as a fastq or sam file, but also provides direct analysis and comparison from specific genomics regions across hundreds or thousands of samples.
In the webinar, we will show examples of configuration and use of the Toolkit for both public SRA and controlled access data associated with studies in the Database of Genotypes and Phenotypes (dbGaP).
Responses will be accepted through March 13, 2015.
This Request for Information (RFI) seeks input regarding the strategic vision for the NLM to ensure that it remains an international leader in biomedical data and health information. In particular, comments are being sought regarding the current value of and future need for NLM programs, resources, research and training efforts, and services (e.g., databases, software, collections) – collectively referred to in this RFI hereafter as “NLM elements”. Your comments can include but are not limited to the following topics:
Current NLM elements that are of the most, or least, value to the research community (including biomedical, clinical, behavioral, health services, public health, and historical researchers) and future capabilities that will be needed to support evolving scientific and technological activities and needs.
Current NLM elements that are of the most, or least, value to health professionals (e.g., those working in health care, emergency response, toxicology, environmental health, and public health) and future capabilities that will be needed to enable health professionals to integrate data and knowledge from biomedical research into effective practice.
Current NLM elements that are of most, or least, value to patients and the public (including students, teachers, and the media) and future capabilities that will be needed to ensure a trusted source for rapid dissemination of health knowledge into the public domain.
Current NLM elements that are of most, or least, value to other libraries, publishers, organizations, companies, and individuals who use NLM data, software tools, and systems in developing and providing value-added or complementary services and products and future capabilities that would facilitate the development of products and services that make use of NLM resources.
How NLM could be better positioned to help address the broader and growing challenges associated with:
Biomedical informatics, “big data”, and data science;
Electronic health records;
Digital publications; or
Other emerging challenges/elements warranting special consideration.
The National Institutes of Health (NIH) developed the NIH Manuscript Submission (NIHMS) system to facilitate the submission of peer-reviewed manuscripts for inclusion in PubMed Central (PMC) in support of the NIH Public Access Policy. Since its inception in 2005, NIHMS has expanded to support the public access policies of other organizations and government agencies (for more details, see the Funders List). The NIHMS system allows users, such as authors, principal investigators, and publishers to supply material for conversion to XML documents in a format that can be ingested by PMC. Depositing a manuscript in NIHMS for inclusion in PMC is a multi-step process, requiring an author to approve the deposited files and associated funding before conversion and the PMC-ready version after conversion.
In May 2014, the National Library of Medicine posted a Request for Information (RFI) asking for ideas on how the National Network of Libraries of Medicine (NN/LM) (http://nnlm.gov) can more effectively and efficiently provide equal access to biomedical information and improve an individual’s access to health information. Based on the feedback from nearly 50 respondents and a review of historical data related to the program, NLM will change the award mechanism for the 2016-2021 Regional Medical Libraries’ cycle from contracts to cooperative agreements. This type of funding mechanism will allow NLM to participate more fully in the work of the RMLs and better coordinate collaborative programs and projects. A Notice of Intent was published on the NIH Grants & Funding site on January 22, 2015.
After nearly 45 years as contracts, the RMLs will return to grants, more specifically cooperative agreements, as the funding mechanism for the 2016-2021 award cycle. Cooperative agreements will allow NLM to actively participate in the work of the RMLs and Centers, enable the RMLs and Centers to better coordinate programs among their Regions and areas of responsibility, and enable the RMLs and Centers to better respond to regional and national needs during the five year grant period. Until the early 1970’s the RMLs were originally funded as grants but transitioned to contracts to allow NLM more oversight and standardization of the work.
NLM is hosting a teleconference Tuesday, January 27, to discuss the decision to go with this award mechanism. NLM will have Extramural Program staff on the call to help get you started if you plan to apply and what you need to do now.
ChemIDplus is a dictionary of over 400,000 chemicals (names, synonyms, and structures). It includes links to NLM and to other databases and resources, including ones to federal, state and international agencies.
1) updated and enhanced content on Decontamination Procedures, Discovering the Event, and Training and Education
2) an NIH CounterACT program funded database with information on twenty-two medical countermeasures (including efficacy, relevant publications, research in progress, FDA and other global regulatory status information)
3) content for how emergency responders can recognize and handle events dealing with toxic gases generated by the combinations of consumer products or common household chemicals
4) a workshop report describing toxic chemical syndromes, or toxidromes, that lays the foundation for a consistent lexicon for use in CHEMM and for other uses that, if adopted widely, will improve response to chemical mass exposure incidents
5) a toxidromes outreach plan whose goal is to raise widespread awareness and encourage use of the toxidromes throughout the stakeholder community, and
6) an evaluation and validation plan for CHEMM’s Intelligent Syndromes Tool (CHEMM-IST) that, once completed, will move CHEMM-IST from its current state as a prototype to a product ready for use in an operational response environment.
CHEMM is a Web-based resource that can be downloaded in advance to Windows and Mac computers to ensure availability during an event if the Internet is not accessible.
CHEMM’s content is also integrated into the NLM Wireless Information System for Emergency Responders (WISER), which is Web-based and downloadable to Windows computers. CHEMM’s content is also available in WISER’s iOS and Android apps. The new CHEMM content will be incorporated into the next release of WISER. http://wiser.nlm.nih.gov/index.html