iFail

Even in the rarefied reaches of the ivory tower, you will find various previously productive scientists with their hands under the table banging on their personal communication devices. In that context, this report on the failure rate of these devices may be of interest. Nonetheless, there does appear to be real functionality that is well suited for scholarly communication and education.

Primary care burdened by primary data

This report out of the Physicians' Foundation shows that doctors are dissatisfied, are going to quit in droves and 94% said the time they devote to non-clinical paperwork in the last three years has increased. So why does it seem that so many are still trying to get into medical school? Is there a medical practice reality chasm?

'Spinning' up the tissues at Harvard

Ever since the late 1990's we have been working on a variety of methods for retrieving data across disparate institutions that are often not even part of the same corporation. In response to an RFA from the National Cancer Institute, called the Shared Pathology Informatics Network, we developed a toolkit that is now in widespread use, specifically to enable genomic and other biological studies on the millions of specimens that are archived across healthcare institutions. As is often the case, we were late in bringing our own tools to use in our own backyard, but that has now happened. The Pathology Specimen Locator (PSL) is now live at our CTSA Catalyst portal. As shown in this screenshot, with authorized credentials, I was able to see that there are over 10,000 lung cancer samples (you can query for any tissue type and disease) across a wide range of ages. It is this sort of IRB-protected, informatics-enabled data liquidity that will accelerate our translational research efforts. Hats off to the entire team but particularly Andy, Frank, John, and Mark.

Transcriptome of a Trio

Hugh Rienhoff will be speaking about an interesting intersection of expression and genetic transmission studies on December 4th.

Thousands of free books

As per the Lexcyle website "Stanza is a free application for your iPhone and iPod Touch. Use it to download from a vast selection of over 40,000 books and periodicals, and read them right on your phone. It’s a wireless electronic library that stays open 24/7." A quick search for science fiction reveals classics by H. G. Wells and pulp fiction by "Doc" E. E. Smith. All without Digital Rights Management. A real treat.

Images in Development

If an image is worth a thousand words, and a video is 30 frames per second, then these movies of a developing zebrafish must be worth millions. I could not conceive now of a course in embryogenesis that did not include these fascinating and wholistic perspectives on the developing organism. What drives those pulses of development, those three- to four-cell cabals, those intricate dances of the somites? Is it all gradients and cell-cell interactions? Or is there a master control program?

Matching high-throughput genomics to high-throughput mining of the literature

In this study (alas, for-fee-access) , Dennis Wall demonstrates how to mine the literature (aka the biomedical bibliome) to focus the analyses of noisy genomic modalities which by virtue of measuring thousands of genes have to be aggressively corrected for multiple hypothesis testing [ed. Disclosure: I am a co-author]. By examining gene expression analyses of individuals with autism through the lens of the prior literature on neuro-psychiatric-behavioral disorders, he is able to identify genes significantly differentially expressed in individuals with autism, both known and previously non-implicated genes. This is one of a growing list of publications that are attempting to match the high throughput qualities of genomic measurements with an equally efficient automated "reading" of all the painstakingly obtained biomedical investigational literature. It also suggests that an even more detailed annotation by librarians of the existing literature (analogously to what the National Library of Medicine has done for years for the broad addition of meta data) will be productively leveraged in future investigations. I suppose this is where my colleagues from the Semantic Web have another opportunity to feed the search engines of Google.

When consent gets in the way

"When consent gets in the way" is the purposefully provocative title of the article (alas, freely open to the public for only 1 month) by Patrick Taylor in which he questions the current dogma about the relationship between consent, privacy, ethical behavior and the public good. Although I was among the early promoters of a strong model of patient personal control of their healthcare data and healthcare decision-making, I found several of Taylor's points compelling. Notably, that "it is questionable whether consent-for-everything will promote privacy and public trust" and "There is more to ethical decision-making than asking whether decisions are made autonomously. Do they take into account virtues, moral values and human narratives with less impoverished conceptions of human freedom? Are the choices good, and do they respect ethical obligations to others?" These points are at the heart of current trends in increasing the "liquidity of patient data" and are certainly central to the business plans of several large companies. How we respond to these assertions as a individuals and a society will be telling. Not only for our research policies and infrastructure but for our conception of healthcare.

E-science = Librarians 2.0?

In this article (free, but requires registration), in The Scientist, we are given another glimpse into the human components of E-science. I'ts one thing to have a distributed computational network capable of delivering teraflops at the tap of a button, it's another thing to have a biological scientific workforce that knows how to use those cycles at all, let alone effectively. Librarians such as our very own David Osterbur, who are also trained in the biological sciences (and particularly in the use of bioinformatics tools) are a remarkably efficient means to help disseminate a working knowledge of these essential tools to our local communities of biological investigators and beyond.

The Joy of Collecting

Every once in a while, I get a notice that reminds me that there are pleasant avocations that don't quite make it to "Reality TV" fare. Here is one such announcement.

Google wins?

Google just settled a lawsuit brought against them by authors and publishers. At first blush, it seems that Google just agreed to spend $125 million to avoid even greater financial liability. But, as Ben Reis pointed out to me, they only had to invest $125M to get the book publishing equivalent of the iTunes store agreed to by a large swathe of publishers. Interesting jujutsu.

Proceeding with precedings

An interesting subfractionation of the open access space is the Nature Precedings. No peer review but broad visibility and the ability to drive a stake in a scientific claim in a very clear way. In many ways this is as revisiting of the Physics preprint service that was among the original drivers of the architecting of the Web.

Plagiarism-proof

With all the concern about plagiarism, it is refreshing to read this essay on the cultivation of creativity and intellectual self-reliance that masquerades as a recipe for plagiarism prevention. Not that it does not outline some ingenious heuristics to prevent plagiarism. It does, by suggesting the assignment of topics that are uniquely at the intersection of the individual's experience and local identity, so as to defy any generality that would allow easy textual cloning to substitute for reflection and crafted writing. It's quite impressive to witness, even if from afar, the dedication to shaping personalized educational experiences that are broadly informed. With such teachers plagiarism really does seem beside the point.

Finally, and most satisfying, is that this essay is a chapter in a fully open access book that is part of an open access series from University of Michigan.

If you can't lick them

This announcement of the purchase of Biomed Central by Springer is interesting. Who is co-opting whom? Is this acknowledgement of the commercial value of the open access model? Or is it the harbinger of spiraling author fees? Regardless of the motivations or goals, the nature of the editorial boards and contributors to Biomed Central is likely to making Springer tread lightly. Else, alternatives will be generated by the increasingly fluid market of publication venues.

Snatching defeat from the open (source) jaws of victory?

I have used Endnote for at least a decade as my primary bibliographic tool, long before it was acquired by Thompson Reuters. If the reporting of a lawsuit brought by Thompson Reuters is correct, then as an academic community we need to seriously reconsider our prior recommendations of the use of a product that seems to now be configured precisely against the emerging fluidity of referencing and hyperlinking encouraged by the web from its outset.

One of the widely recognized successes of the Web was indeed in its dissemination of several decades of developments in hyperlinking that allowed, among other uses, different sources of knowledge and information to be hyperlinked. The occasionally wobbly efforts in deploying a Semantic Web that includes some minimalistic formalism of knowledge representation constitute an important and worthy attempt to make such hyperlinking and annotation even more efficient and productive. So, when Thompson starts suing open sourced efforts (using Semantic Web standards) to interoperate with the Endnote bibliographic styles, it is (again if the reports are accurate) creating obstacles to the free flow of information between the richly growing ecosystem of reference and bibliographic applications (web-based or otherwise). This runs counter to all the trends in open source publishing and widely shared document formats.

If indeed, I have misunderstood the nature of the lawsuit then I will readily and publicly retract these comments in this forum. Otherwise, those of us who want our students and colleagues to be able to freely exchange their bibliographic data will consider some alternatives.

Academia can lead in setting the example for sharing of research data

This article summarizes the benefits of data sharing for research and makes a few common sense recommendations (excerpted below). If our leading academic health centers would adopt these, the yield to all of us (as consumers of research) of our investment in research would grow rapidly.

RECOMMENDATIONS FOR ACADEMIC HEALTH CENTERS TO ENCOURAGE DATA SHARING

1. Commit to sharing research data as openly as possible, given privacy constraints. Streamline IRB, technology transfer, and information technology policies and procedures accordingly.
2. Recognize data sharing contributions in hiring and promotion decisions, perhaps as a bonus to a publication's impact factor. Use concrete metrics when available.
3. Educate trainees and current investigators on responsible data sharing and reuse practices through class work, mentorship, and professional development. Promote a framework for deciding upon appropriate data sharing mechanisms.
4. Encourage data sharing practices as part of publication policies. Lobby for explicit and enforceable policies in journal and conference instructions, to both authors and peer reviewers.
5. Encourage data sharing plans as part of funding policies. Lobby for appropriate data sharing requirements by funders, and recommend that they assess a proposal's data sharing plan as part of its scientific contribution.
6. Fund the costs of data sharing, support for repositories, adoption of sharing infrastructure and metrics, and research into best practices through federal grants and AHC funds.
7. Publish experiences in data sharing to facilitate the exchange of best practices.

Unnecessary thievery

Several years ago, I was working on modeling the hypothalamic-pituitary axis with my colleague Joe Gonzalez-Heydrich. Unsurprisingly, we could not find any primary data in articles ostensibly describing the relationship between various hormones of this axis. So, I found a very nice shareware program called DataThief. DataThief is "a program to extract (reverse engineer) data points from a graph. Typically, you scan a graph from a publication, load it into DataThief, and save the resulting coordinates, so you can use them in calculations or graphs that include your own data." It worked as billed and recently when I was working with my colleague Asher Schacter on predicting outcomes of drug development from pre-clinical data, I remembered how useful DataThief had been and recommended that he use it to extract the primary data from publications for each of the pharmaceuticals he wanted to study. Lo and behold, it worked again!

If only we had a policy in place that required that all primary data be deposited in a public electronic repository or repositories, then this additional, laborious, and time-consuming step would be unnecessary. Bioinformaticians have been very effective in demonstrating the value of sharing primary experimental data (e.g. high throughput data such as gene expression data or gene variant data) but clinical researchers have yet to achieve the same enlightenment. Until then, please make sure your graphs are very accurate in your publications so that others may benefit from your hard work and the taxpayers' investments in your research.

BLAST this!

David Osterbur often gives extremely well received lectures on the use of public bioinformatics resources for biologists. However, even he is limited in how many audiences he can reach. So, if you know of a biologist who needs some help in the use of BLAST, or the UCSC Genome Browser or even in the search of information regarding herbs and dietary supplements, you will be happy to know that the Countway Library (in collaboration with the MIT Engineering and Sciences Libraries) has made available several instructional videos. Let me know if these are helpful and if you'd like to see more (and about what).

Out of date but not dated?

This is a great example of how the instant-at-hand-reflexive-cut-and-paste nature of electronic information can bridge the virtual to inflict real harm. Contemplate how clinical out-of-date information can be similarly used to boost the medical malpractice of the incidentalome. Will medical libraries step up to the challenge of keeping the medical profession up to date?

[Thanks to Ben Reis for the pointer]

The Harvard Catalyst site is live and open

The name of the Harvard University Clinical and Translational Science Center is Catalyst. Several of its resources are publicly available. For example, you can now see the biomedical scholarly output of our university at a glance. You can find people, buildings, phone numbers, directions and parking across the entire University (!) with 18+ participating institutions. You can see the influenza risk across our local geography and recent history. You can explore which clinical trials are supported by the institutions across Catalyst. You can use Webdash to share web pages and publications and their citations with collaborators and colleagues. You can browse and search the available Core facilities (in the hundreds). And if you need analytic help you can reach out to the Catalyst biostatistics program and genetics program, for example. Within a year, we will reveal the data sharing function called SHRINE which allows authorized users to study patient populations (with regulatory oversight) for pharmacovigilance, and various clinical research projects (e.g genome-wide studies of asthma, major depression resistant to standard antidepressants).

This site is the collaborative effort of multiple informatics groups in our community, including HMS Center for Biomedical Informatics, HMS IT, and the IT groups of Partners Healthcare Systems, Beth Israel Deaconess Medical Center, and Children's Hospital. It was an impressive 107 day dash bringing together diverse applications into one package. It's still rough and in progress and I would welcome your comments as would our Research Navigators.

Just some cocktail party conversation for you: Note the relative decline of protein research (relative to other topics) in the past decade at our University. The same indicators (gratifyingly) show the rise of mathematical topics in our life sciences scholarly output. Our most prolific author is Walt Willet (note the alternate ways his name appears each with its own publication history: to be fixed in the next iteration of Medvane). Note that JBC appears to be a popular journal for our authors to publish in.