Call for task force members – BioCaddie (BD2K – DDIC)

Posted on November 21st, 2014 in Anita Bandrowski, News & Events | No Comments »

As part of the NIH’s Big Data to Knowledge (BD2K) kick off, we are pleased to announce the launch of the Data Discovery Index Consortium, bioCADDIE ( bioCADDIE (biomedical and healthCAre Data Discovery and Indexing Ecosystem) was established to help define requirements for building a Data Discovery Index to make it easier for researchers to find, access, reuse and share data. bioCADDIE will be engaging the community through task forces and funding small pilot projects to explore the best ways to search for, access and cite data from NIH-funded researchers.

We are inviting community members to join bioCADDIE task forces.

For more information please visit bioCADDIE website.

INCF & NIF social – Monday night in DC

Posted on November 12th, 2014 in Anita Bandrowski, News & Events | No Comments »

NIF and INCF are present at Neuroscience 2014 in Washington DC, November 15-19 at the Walter E Washington Convention Center. Please visit us in booth #3516 & #3517, located near other neuroinformatics exhibitors (see map: Are you working on an interesting project, or maybe looking for new collaborators? Come by and talk to us!

Neuroscience tools and projects demos at the INCF booth
For the eight year running, we are hosting neuroinformatics demonstrations in our booth during all exhibition days. Tools and projects from INCF Programs, National Nodes and community will be presented. You can find the schedule and demo abstracts on our webpage via the following links:
* Demo schedule:
* Demo abstracts:

Monday Nov 17 Neuroinformatics social with INCF, NIF and NITRC
On Monday November 17, 17:30 – 19:30, we will be hosting a social together with NIF and NITRC, at the Cuba Libre Restaurant & Rum bar on 801 9th St. NW (the corner of 9th & H Streets NW) in the Penn Quarter neighbourhood of Washington DC. Drinks and finger food will be served – come by and mingle!

You can also follow us on Twitter (; we will be posting regular updates all through the meeting.

Hope to see you in Washington!

From Force11: Abstract deadline in 5 days for Force2015

Posted on November 10th, 2014 in Anita Bandrowski, General information, News & Events | No Comments »


  • New! Travel Fellowship Applications Open
  • New! Call for Vision Flash Talk Submissions Open
  • Call for Session Abstracts Submission Deadline November 15
  • Call for Demo/Posters Submission Deadline December 1
  • Call for Pre-Conference Workshop Submissions
  • Registration
The FORCE2015 Research Communication and e-Scholarship Conference (FORCE2015) will be held 12-13 January, 2015 at the University of Oxford, UK. FORCE2015, the successor of the Beyond-the-PDF conferences, will bring together resesearchers, scholars, librarians, archivists, information scientists, publishers, and research funder in a lively forum.

NEW! Travel fellowships applications – Deadline December 1, 2014

Travel fellowships are available for students, Post-docs and scholars from developing nations.

NEW! Flash Vision Session: Deadline December 1, 2014

This is your chance to get your idea on the map and help change the future of scholarly communication. Submissions are invited from anyone in attendance to give a 5 min, 3 slide pitch on your idea.

Call for Session Abstracts – Deadline November 15,
Submit your abstracts for the “Valuing the Diversity of Scholarly Impact in a Networked World” and“Credit Where Credit is Due” Sessions.

Call for posters and demos – Deadline December 1, 2014
Show what the future of research and how new technologies are shaping the way scholarship is being done, reported and pushed forward. Present a poster or demonstration.

Call for Pre-Conference Workshops
On the preceding day, 11 January 2015, there will be workshops, informal and formal collaborations, and business meetings associated with the main conference. You may submit requests for hosting a meeting on Sunday.

Registration – Discount registration Deadline December 15,

We hope to see you there!

Big Data vs Small Data: Is it really about size?

Posted on October 31st, 2014 in Anita Bandrowski, Curation, Data Spotlight, Inside NIF, Interoperability | No Comments »

We have been hearing for some time that when it comes to data, it is all about size. The bigger is better mantra has been all over the press, but is it really size that matters?

There are the so called “Big Data” projects such as the Allen Brain Atlas, which generates data, sans hypothesis, over the whole brain for thousands of genes. This is great because the goal of the project is to generate consistent data and not worry about which disease will or will not be impacted by each data point. That may be a great new paradigm for science, but there are not many projects like this “in the wild”.

Most data is being generated in the world of science can be considered small, i.e., would fit on a personal computer, and there are a LOT of labs out there generating this sort of data. So the question that we addressed in the recent the Big Data issue of Nature Neuroscience, is whether small data could organize to become big data? If such a thing is desirable, then what would be the steps to accomplish this lumping?

Here are the principles that we have extracted from working on NIF that we think will really help small data (from Box 2):

Discoverable. Data must be modeled and hosted in a way that they can be discovered through search. Many data, particularly those in dynamic databases, are considered to be part of the ‘hidden web’, that is, they are opaque to search engines such as Google. Authors should make their metadata and data understandable and searchable, (for example, use recognized standards when possible, avoid special characters and non-standard abbreviations), ensure the integrity of all links and provide a persistent identifier (for example, a DOI).

Accessible. When discovered, data can be interrogated. Data and related materials should be available through a variety of methods including download and computational access via the Cloud or web services. Access rights to data should be clearly specified, ideally in a machine-readable form.

Intelligible. Data can be read and understood by both human and machine. Sufficient metadata and context description should be provided to facilitate reuse decisions. Standard nomenclature should be used, ideally derived from a community or domain ontology, to make it machine readable.

Assessable. The reliability of data sources can be evaluated. Authors should ensure that repositories and data links contain sufficient provenance information so that a user can verify the source of the data.

Useable. Data can be reused. Authors should ensure that the data are actionable, for example, that they are in a format in which they can be used without conversion or that they can readily be converted. In general, PDF is not a good format for sharing data. Licenses should make data available with as few restrictions as possible for researchers. Data in the laboratory should be managed as if it is meant to be shared; many research libraries now have data-management programs that can help.


RISE program at NMSU, highlighting success

Posted on October 21st, 2014 in Anita Bandrowski, Author, General information, News & Events | No Comments »

We at NIF were very fortunate to have hosted the director of the RISE program from NMSU, Elba Serrano this summer attempting to develop coursework and improve outreach to students and faculty at New Mexico State. We believe that the scientific workforce in the coming decade will need to be aware of computational problems, statistics and bioinformatics resources. It is critical that we train this workforce and the RISE program is exactly the right place to start.

We are thrilled that this collaboration has resulted in a set of workshops that will be held in the spring and a set of course modifications for NMSU students to start becoming aware of bioinformatics in the fall.

A news story outlining the success of the program can be found below; a 90% promotion rate of minority and disadvantaged students is truly something to be proud of!


Please join us for a webinar discussing Neurostars: A Q&A platform for neuroscience

Posted on October 20th, 2014 in Anita Bandrowski, Author, News & Events, Webinar Announcement | No Comments »

Next week we kick off the fall webinar series, with Dr. Satrajit Ghosh from the Massachusetts Institute of Technology. Dr. Ghosh is a research scientist at the mcgovern institute for brain research and an assistant professor at harvard medical school. He will talk about Neurostars and Biostars.

Neurostars ( and Biostars ( are sibling question and answer platforms for neuroscience and bioinformatics communities. Based on the successful StackOverflow model, these platforms provide a voting mechanism, a modern user-interface, integrated search, and personalization characteristics that are typically not available in traditional mailing lists or forums. It also supports facilities for data discovery links and discussion using the bittorrent mechanism, and is now part of the mozilla science lab ( Neurostars is maintained and run by the International Neuroinformatics Coordinating Facilities (INCF) with community input and support.

This webinar will go over some of the basic operations, some features that are only available on these platforms, and finish with a near term roadmap of new features under consideration.


Available here:

When: Anytime!

Network of BioThings Hackathon – Nov 7-9

Posted on October 16th, 2014 in Anita Bandrowski, News & Events | No Comments »

The Network of BioThings is sponsoring a hackathon.
NoB Hackathon poster

Come one, come all.
Mainly though, sign up because space is fairly limited.


Posted on October 10th, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

NIF applauds ISIS pharmaceuticals, the press release is below. This is an event, unfortunately too rare, where neuroscience research is successfully pushed from the bench to a clinical application giving an option for treatment of babies diagnosed with this neuro-skeletal disorder. We salute the SMA foundation, which has been pushing scientists, clinicians and the public for years, breaking down the obstacles to move basic science and the pharmaceutical industry toward a collaboration around a rare genetic disease.

—————————-Press Release Below ————————————
Phase 3 ENDEAR study in infants with SMA enrolling; on track to initiate Phase 3 study in children with SMA later this year

Isis to host a webcast at 11:30 a.m. EDT on Friday, October 10
CARLSBAD, Calif., October 10, 2014 – Isis Pharmaceuticals, Inc. (NASDAQ: ISIS) today provided an update on its ongoing open-label Phase 2 clinical studies of ISIS-SMNRx in infants and children with spinal muscular atrophy (SMA) at the 19th International World Muscle Society (WMS) Congress in Berlin, Germany. Isis is currently treating infants with SMA with ISIS-SMNRx in a Phase 3 study called ENDEAR, and plans to initiate a second Phase 3 study, called CHERISH, in children with SMA later this year.
“I am encouraged with the totality of the data presented today, which show that median event-free ages for SMA infants in both the 6 mg and 12 mg cohorts compare favorably to that observed in a recent natural history study. These data combined with the safety and tolerability profile observed to date support my enthusiasm to further evaluate ISIS-SMNRx in a Phase 3 study in infants with Type I SMA,” said Richard Finkel, M.D., chief, division of neurology, department of pediatrics, Nemours Children’s Hospital. “Often infants with Type I SMA succumb to early death due to progressive weakness of the muscles responsible for breathing and feeding. In the PNCR natural history study, for which I was the lead investigator, in a group of untreated patients similar to those in the Isis Phase 2 study, the median event-free age was 10.5 months, with less than 20% of patients event free at 18 months. In addition to the positive data on event-free survival, substantial and persistent increases in muscle function as measured by the CHOP INTEND and Hammersmith Infant Neurological Examination were also observed in ISIS-SMNRx-treated infants up to 9 months on study. This is an important finding because in general, infants with Type I SMA decline over time in their motor function as reflected in scores on these tests.”
Event-free survival data from Phase 2 study in infants with SMA
In the Phase 2 study in infants with SMA, a total of 20 infants were dosed as of Sept 1st, four infants in the 6 mg cohort and 16 infants in the 12 mg cohort. As of April 7, 2014, the date of Isis’ previous data update, the per protocol efficacy populations (PPEP) (patients who completed the three dose induction regimen in the study) constituted four patients in the 6 mg and seven patients in the 12 mg dose cohorts,. As of September 2, 2014, the date for this data update, the PPEP constituted four patients in the 6 mg and 12 patients in the 12 mg dose cohorts.
In the 6 mg cohort:
•          No patients have had an event (death or permanent ventilation) since April 2014. As of September 2, 2014, there have been two events (one accidental death and one permanent ventilation) in the 6 mg cohort.
•          Isis previously reported a median event-free age of 14 months for the infants in the PPEP on April 7, 2014. The median event-free age on September 2, 2014 for the infants in this group is now 16.3 months.
In the 12 mg cohort:
•          Dosing in the 12 mg cohort began five months after the initiation of dosing for the 6 mg cohort. As a result, the patients in the 12 mg cohort have participated in the study for a shorter time than those in the 6 mg cohort. As of April 7, the PPEP in the 12 mg dose cohort contained 7 infants. As ofSeptember 2, the PPEP for the 12 mg dose cohort contained 12 infants, which included an additional five infants who had more recently entered the study.
•          Isis previously reported a median event-free age of 9.6 months for the infants who constituted the 12 mg PPEP as of April 7, 2014. The median event-free age at September 2, 2014 for these infants is now 13.8 months.
•          The median event-free age of the 12 infants in the PPEP as of September 2, 2014 for the 12 mg cohort is 11.6 months. Of these 12 infants, nine are alive without the need for permanent ventilation.
•          As of September 2, 2014, there have been four events (one permanent ventilation and three deaths, all related to respiratory infections) in the 16 infants from the 12 mg cohort.
Increases in muscle function scores in this study in infants with SMA
Measures of muscle function are also being assessed in this study. Increases in muscle function scores were observed in infants in both dosing cohorts using the Children’s Hospital of Philadelphia Infant Test of Neuromuscular Disorders (CHOP INTEND), a motor assessment test that is used to evaluate muscle strength in infants with SMA.
•          Increases in CHOP INTEND scores occurred in a majority of infants in the study. Infants in the PPEP from the 6 mg and 12 mg cohorts combined showed mean increases from baseline in CHOP INTEND of 9.3 points with 14 of the 16 infants showing an increase in CHOP INTEND scores.
•          Infants from the 12 mg dose cohort PPEP showed mean increases from baseline in CHOP INTEND of 11.7 points with 11 of the 12 infants showing an increase in CHOP INTEND scores.
Developmental milestones are also being examined in this study using the Motor Milestones portion of the Hammersmith Infant Neurological Examination, with 14 out of the 16 infants in the combined PPEP exhibiting improvements in motor milestones.
The safety and tolerability profile of ISIS-SMNRx to date supports continued development. As of September 2, 2014, 20 infants have been exposed to doses of either 6 mg or 12 mg of ISIS-SMNRx for a total of 67 intrathecal injections. The lumbar puncture procedure in SMA infants has been well tolerated and shown to be feasible. In all infants dosed, there have been no drug-related serious adverse events. Most of the adverse events (non-SAEs) have been mild or moderate in severity and not related to drug. There were no changes in the safety profile with repeated doses of ISIS-SMNRx.
Clinical data on ISIS-SMNRx Mechanism of Action
Today, Isis reported the results from an analysis of spinal cord tissue samples from autopsies showing that ISIS-SMNRx is distributed throughout the central nervous system. The results of these analyses also showed greater levels of full length SMN2 mRNA and full length SMN protein in tissues in ISIS-SMNRx-treated SMA infants compared to the levels of SMN2 mRNA and full length SMN protein in the tissues analyzed from untreated SMA infants. These analyses were conducted on tissue samples collected in three infants who had received three or more doses of ISIS-SMNRx and were compared to tissue samples from four untreated SMA infants and three infants without SMA at a similar age range.
•          Analysis of spinal cord tissue showed that ISIS-SMNRx concentration in spinal cord tissues was greater than the concentration that resulted in biological activity in animal studies. ISIS-SMNRx was found in multiple segments of the spinal cord and brain and in motor neurons.
•          Greater level of full-length (containing exon 7) SMN2 mRNA was observed in the spinal cord and brain tissue of ISIS-SMNRx-treated SMA infants compared to the level of full-length SMN2 mRNA in the untreated SMA infants.
•          In patients treated with ISIS-SMNRx, greater amounts of SMN protein were observed in the spinal cord compared to the amount of SMN protein observed in the untreated SMA infants.
•          SMN protein was observed in neurons of tissues analyzed in ISIS-SMNRx-treated SMA infants in which ISIS-SMNRx was present.
“The results on ISIS-SMNRx presented today forms an encouraging profile of a potential new therapy for patients with SMA,” continued Dr. Finkel. “The consistency of observations in event-free survival, CHOP-INTEND and development milestones, combined with the clinical data supporting the mechanism of action by which ISIS-SMNRx was designed to act, creates strong support to continue evaluation of ISIS-SMNRx.”
“We are encouraged that we have been able to evaluate both the distribution of ISIS-SMNRx in spinal cord tissues and motor neurons, and the levels of full length SMN protein in the spinal cord of ISIS-SMNRx-treated infants. We are very fortunate to have access to these tissue samples, and thankful to the families who have allowed us to use them to advance the study of SMA and ISIS-SMNRx. Access to these tissues has enabled us to confirm what we observed in our earlier preclinical work; that ISIS-SMNRx is broadly distributed throughout the central nervous system of ISIS-SMNRx-treated infants. We are also pleased to observe that the levels of ISIS-SMNRx in tissues analyzed from ISIS-SMNRx-treated infants are greater than the concentrations at which we observed biological activity in our animal studies. We are also encouraged with the greater levels of full-length SMN2 mRNA and commensurate increases in SMN protein we observed in tissues analyzed from ISIS-SMNRx-treated SMA infants as compared to the levels of full-length SMN2 mRNA and SMN protein we observed in tissues analyzed from untreated SMA infants,” said C. Frank Bennett, Ph.D., senior vice president of research at Isis Pharmaceuticals.
Results from Phase 2 study in children with SMA
In the ongoing, open-label study in children with SMA, increases in muscle function scores, as measured by the Hammersmith Functional Motor Scale-Expanded (HFMSE), were observed in children treated with multiple-doses of ISIS-SMNRx. As previously reported in April 2014, children in the 3 mg, 6 mg and 9 mg cohorts achieved mean increases from baseline of 1.5, 2.3 and 3.7 points, respectively, 9 months following their first dose (six months after last dose). Further evaluation of these children showed that the previously observed mean increases in muscle function scores continued to show increases from baseline for an extended period after their last dose with mean increases from baseline of 1.7, 3.2 and 2.3, respectively, eight to 13 months after last dose.
Increases in two additional functional tests were also observed eight to 13 months after last dose in the six-minute walk test (6MWT) and the upper limb mobility (ULM) test. In the 6MWT, performed with 10 ambulatory children, a mean increase of 24.4 meters was observed 12 to 16 months after the patients’ baseline visits, compared to the previously reported increase of 22.7 meters at nine months. In the ULM test, a mean increase of 3.1 points was observed 11 to 16 months after the patients’ baseline visits, compared to the previously reported increase of 2.3 points at nine months.
The safety and tolerability profile of ISIS-SMNRx continues to support continued development. As of September 2, 2014, 56 children have been exposed to doses ranging from 1 mg to 12 mg of ISIS-SMNRx. The majority of these children have received multiple doses of drug and in total 183 doses of ISIS-SMNRx have been administered. The lumbar puncture procedure in SMA children has been well tolerated and shown to be feasible. In all children dosed, there have been no drug-related serious adverse events. Most of the adverse events (non-SAEs) have been mild or moderate in severity and not related to drug. There were no changes in the safety profile with repeated doses of ISIS-SMNRx.
“SMA is a heartbreaking disease. Children with SMA are bright and engaging, but due to progressive muscle weakness, grow weaker over time and suffer a decline in their physical abilities. Because of the inevitable gradual decline that patients with SMA exhibit, I am encouraged with the consistency of the muscle function scores in these children. Not only do these children experience increases in muscle function scores, even after a single dose of ISIS-SMNRx, but it now appears that these increases can be sustained for a significant time after dosing,” said Basil Darras, M.D., professor of neurology, director of clinical neurology at the Boston Children’s Hospital and Harvard Medical School.
“The consistency of the increases in muscle function scores across different SMA patient populations, including both children and infants with SMA, and the dose-and time-dependency of these increases is encouraging. The observation of increases in SMN protein in the spinal cord in tissues analyzed from ISIS-SMNRx-treated infants, suggest that ISIS-SMNRx is acting by the mechanism of action through which it was designed to act,” concluded Dr. Bennett.
Investor Event
At 11:30 a.m. Eastern Time, Oct. 10, 2014, Isis will conduct a webcast to discuss ISIS-SMNRx data presented at the WMS. A live audio webcast of the presentation will be available on the “Investors & Media” section of the Company’s website, A replay will be available for a limited time. The slides presented at the WMS meeting are available on Isis’ website at
ISIS-SMNRx is designed to alter the splicing of a closely related gene (SMN2) to increase production of fully functional SMN protein. The United States Food and Drug Administration granted orphan drug status and fast track designation to ISIS-SMNRx for the treatment of patients with SMA. Isis is currently in collaboration with Biogen Idec to develop and potentially commercialize the investigational compound, ISIS-SMNRx, to treat all types of SMA. Under the terms of the January 2012 agreement, Isis is responsible for global development and Biogen Idec has the option to license the compound until completion of the first successful Phase 2/3 study or the completion of two Phase 2/3 studies.
ISIS-SMNRx is being evaluated in a pivotal Phase 3 study, ENDEAR, in infants with SMA. The ENDEAR study is a randomized, double-blind, sham-procedure controlled thirteen month study in approximately 110 infants diagnosed with SMA. The study will evaluate the efficacy and safety of a 12 mg dose of ISIS-SMNRxwith a primary endpoint of survival or permanent ventilation. Additional efficacy endpoints are also included in the study. For further study information, please visit and search for ISIS-SMNRx or the identifier number NCT02193074 or visit the ISIS-SMNRx study site at
Isis acknowledges support from the following organizations for ISIS-SMNRx: Muscular Dystrophy Association, SMA Foundation, Cure SMA and intellectual property licensed from Cold Spring Harbor Laboratory and the University of Massachusetts Medical School.
SMA is a severe genetic disease that affects approximately 30,000-35,000 patients in the United States, Europe and Japan. SMA is caused by a loss of, or defect in, the survival motor neuron 1 (SMN1) gene leading to a decrease in the survival motor neuron (SMN) protein. SMN is critical to the health and survival of nerve cells in the spinal cord responsible for neuromuscular growth and function. One in 50 people, the equivalent of about six million people in the United States, are carriers of a defective SMN1 gene, which is unable to produce fully functional SMN protein. Carriers experience no symptoms and do not develop the disease. However, when both parents are carriers, there is a one in four chance that their child will have SMA. The severity of SMA correlates with the amount of SMN protein. Infants with Type I SMA, the most severe form of the disease, produce very little SMN protein and have a life expectancy of less than two years. Children with Type II have greater amounts of SMN protein but still have a shortened lifespan and are never able to stand independently. Children with Type III have a normal lifespan but accumulate life-long physical disabilities as they grow.
Biogen Idec and Isis have established four collaborations focused on leveraging antisense technology to advance the treatment of neurological and neuromuscular disorders. This alliance combines Isis’s expertise in antisense technology to evaluate potential neurological targets and discover antisense drugs with Biogen Idec’s capability to develop therapies for neurological disorders. Isis is primarily responsible for drug discovery and early development of antisense therapies. Biogen Idec has the option to license each antisense program at a particular stage in development. Current development-stage programs include antisense drugs to treat SMA, ISIS-SMNRx, and myotonic dystrophy type 1, ISIS-DMPKRx.
Isis is exploiting its leadership position in antisense technology to discover and develop novel drugs for its product pipeline and for its partners. Isis’ broad pipeline consists of 32 drugs to treat a wide variety of diseases with an emphasis on cardiovascular, metabolic, severe and rare diseases, including neurological disorders, and cancer. Isis’ partner, Genzyme, is commercializing Isis’ lead product, KYNAMRO®, in the United States for the treatment of patients with HoFH. Isis’ patents provide strong and extensive protection for its drugs and technology. Additional information about Isis is available at
This press release includes forward-looking statements regarding Isis’ alliance with Biogen Idec, the discovery, development, activity, therapeutic and commercial potential and safety of ISIS-SMNRx and the discovery, development and therapeutic potential of an antisense drug for the treatment of spinal muscular atrophy. Any statement describing Isis’ goals, expectations, financial or other projections, intentions or beliefs is a forward-looking statement and should be considered an at-risk statement. Such statements are subject to certain risks and uncertainties, particularly those inherent in the process of discovering, developing and commercializing drugs that are safe and effective for use as human therapeutics, and in the endeavor of building a business around such drugs. Isis’ forward-looking statements also involve assumptions that, if they never materialize or prove correct, could cause its results to differ materially from those expressed or implied by such forward-looking statements. Although Isis’ forward-looking statements reflect the good faith judgment of its management, these statements are based only on facts and factors currently known by Isis. As a result, you are cautioned not to rely on these forward-looking statements. These and other risks concerning Isis’ programs are described in additional detail in Isis’ annual report on Form 10-K for the year ended December 31, 2013, and its most recent quarterly report on Form 10-Q, which are on file with the SEC. Copies of these and other documents are available from the Company.
In this press release, unless the context requires otherwise, “Isis,” “Company,” “we,” “our,” and “us” refers to Isis Pharmaceuticals and its subsidiaries.
Isis Pharmaceuticals® is a registered trademark of Isis Pharmaceuticals, Inc. KYNAMRO® is a registered trademark of Genzyme Corporation.
Isis Pharmaceuticals’ Contacts:
D. Wade Walke, Ph.D.                                                 Amy Blackley, Ph.D.
Vice President, Corporate Communications and          Associate Director, Corporate Communications
Investor Relations                                                        760-603-2772

Introducing the Aging Portal

Posted on October 8th, 2014 in Anita Bandrowski, Data Spotlight | No Comments »

The Neuroscience Information Framework, has been asked many times “how can we sort through this dizzying amount of data?” to which we have never had a great answer until now. With SciCrunch, a shared portal infrastructure that allows users to create their own portals into subsets of data, NIF has created a dedicated subset of resources funded by and of interest to the aging research community.

The portal can be found here:


The NIA funded a small award to pull interesting resources out of the main, at times overwhelming quantity, of NIF resources into their own portal, and we have done this for 14 databases including the following that were brought in specifically for the portal:

Aging Genes and Interventions Database


Human Mortality Database

Lifespan Observation Database


Other resources that were already present in the Data Federation such as Aging Genes Database and Clinical Trials. However, we hypothesize that with many databases only subsets of the data are relevant to aging, for example our integrated Clinical Trials data are relevant to aging when the population is aged. Similarly Gene Ontology Annotations for aging-related genes are included. If this is not a valid assumption, we would love to hear from you.

We hope that this portal is a useful tool for aging researchers, who can start looking for aging relevant data or databases funded by the NIA by looking at the subset of community databases and hopefully recover reasonable subsets of data. However, if the subset of data is not sufficient for the purposes of the researcher, all of the other databases aggregated by NIF are available and accessible via a fully configured search interface under the “more resources” tab.


Happy Data Hunting!

NIF now pleased to serve more electrophysiology data

Posted on September 30th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | 1 Comment »

For years, physiology has been lagging far behind anatomy as data sharing is still in infancy in that community as opposed to being fairly standard now in neuro-anatomy.

We are pleased to announce that the Physiobank registry resource from MIT, containing data from a set of physiology experiments has been added to the NIF Data Federation.


This brings us to 6 sources of data (anatomy is still winning, but perhaps we can change that)

CRCNS, a repository of e-phys data (patch clamp mostly)

NeuroElectro, a rather large listing of cellular properties mined from e-phys papers

NeuronDB, a curated set of e-phys properties of known cell types including currents, receptors and transmitters

EEG-base, a repository of EEG data

Neurodatabase, a repository of extracellular data sets.


Note, this list may be incomplete because it does not include Model data, so please see Integrated Models, a virtual database currently indexing computational models from:ModelDBOpen Source BrainSimTK and  CellML.