From the lab to scientific publishing to clinical solutions, the Open Access movement is changing the way science advances
(Guest post by Joseph Jackson)
The 2nd Open Science Summit is the weekend of October 22-23, 2011 at the Computer History Museum in Mountain View, just before the 2011 Open Access (OA) week, which runs October 24th-28th. Open Science evokes different associations for different people, depending on which part of the scientific process they most regularly engage with. One critical component focuses on access to scientific literature. The OA movement has made great strides in the last ten years with the creation and maturation of journals and publishers like PLoS and Biomed Central.
But the most critical shifts toward Open Science arguably are happening in the life sciences. The technological revolution underway in next generation sequencing is enabling, but also requiring bold new collaborative approaches to manage increasing complexity and accelerate the translation of scientific discoveries into desperately needed therapies.
Finally, the moment we’ve all been waiting for, a standing ovation for …. Kelly Bouchonville! Congratulations to NextBio’s first place Travel Grant winner!
Effective communication of data is one of the most important and also most overlooked aspects of any research career. In an age of digital technology and free and instant access to databases containing a plethora of information, it is vital that one be able to easily interpret and assemble that data. No longer is it enough to look at data from a single species and/or experiment. One must broaden the scope to look at effects seen in a broad array of organisms and/or experiments carried out under a range of conditions. Additionally, many research outcomes are no longer single gene-centric, but must take entire pathways and systems into account.
As a graduate student nearing completion of a Ph.D., it has become increasingly important to be able to integrate data from numerous studies, both in a variety of conditions for my organism of choice and for single genes/proteins of interest in a range of organisms. The tools available through NextBio have simplified some parts of the integration process. Additionally, NextBio tools facilitate broadening the implications of results by providing correlations and additional studies of interest, making it easy to see how specific results in one organism translate into an adverse effect in another organism.
A big round of applause please for… Elena Piskounova! Congratulations to NextBio’s second place Travel Grant winner!
One of the main interests of my PhD work has been a subset of the Argonaute family of proteins called the Piwi proteins. Piwi proteins have been shown to play a key role in male germ cell maintenance and to function with a novel class of small non-coding RNAs called piRNAs (Piwi-interacting RNAs). However, the mechanisms by which Piwi proteins control transposable elements and DNA methylation have not been completely elucidated.
When I was introduced to the capabilities of NextBio, there were several key features that I found particularly useful. I first performed a simple search for the different members of the Piwi protein subfamily. I was particularly struck by the convenient organization of the search results, allowing me to see the instances in which the different Piwi genes have been analyzed in various tissues, diseases, as well as drug studies. This has given me insight into the various systems that are being used to study Piwi proteins. Furthermore, delving deeper into these results allowed me to identify the less obvious studies that did not truly focus on Piwi proteins, yet contained valuable information on their regulation nonetheless.
Drum roll please… Congratulations, Bibhash Mukhopadhyay, and thanks to all participants for entering.
NextBio: A versatile one-stop-shop for researchers (and a data junkie’s paradise)!
I am currently writing my doctoral dissertation on a gene involved in retinal degeneration at Baylor College of Medicine, and I have had internship experience. Both of these responsibilities involve assimilation and organization of a large amount of information to create mental snapshots that can be recalled and applied to specific contexts that I am interested in looking at. For my dissertation, I need to interpret primary research data in the context of existing literature or “knowledge base”, whereas the internship required integration of technical and clinical data for enumerating commercial utility.
by Hope Leman
Guest Blogger Hope Leman: Hope Leman is a Research Information Technologist at the Samaritan Health Services Center for Health Research and Quality, co-founder of Next Generation Science, a staff writer at AltSearchEngines and the Web administrator of ScanGrants. You can find her on NextBio, FriendFeed and Twitter.
Review of Internet Cool Tools for Physicians by Melissa L. Rethlefsen, David L. Rothman and Daniel S. Mojon
Okay, this is going to one of those book reviews full of praise and every conceivable adjective connoting the concept of “must-read.” And don’t be put of by the cutesy use of “cool” in the title—this is a book of substance and not just for physicians, either. Anyone interested in the provision of health information on the Internet should buy a copy of this book and certainly all public libraries should have it on their shelves. Even experienced medical librarians should at least page through it. I can think offhand of quite a number of professionals and students who would benefit from reading it: nurse researchers, pharmacists, physical therapists, dentists, medical students, nursing students, anyone who does any sort of health sciences research. And given the rise of increasingly sophisticated laypeople as typified by the term e-patient there is a need for well-written, authoritative books such as this one that discuss how to find health information beyond Google, MedlinePlus and Wikipedia.
- Hope Leman
As I try to grasp the revolution in scientific and medial research that Science 2.0 and Medicine 2.0 are effecting I often find that I am literally being rendered sleepless by trying to keep up on the writings of the leading thinkers on the subject such as Cameron Neylon, Jean-Claude Bradley, Michael Nielsen and the new kid on the block, Steve Koch.
It is quite daunting to try to keep up with the many fascinating things they have to say and the many links they provide to their colleagues in the field such as Bill Hooker and Rich Apodaca (How I wish that the latter two would add “Follow me on Twitter” buttons to their blogs. They have fascinating things to say and I find that the best way by far to keep up with thinkers and doers is via Twitter. RSS is so 2006.)
– Steve Koch
Thank you, Lisa, for inviting me to post a blog here! In thinking about what to write, I noticed two previous entries on this blog: the first was one by Lisa discussing Francis Collins possibly being the next director of the NIH. Francis Collins was the leader of the wildly successful, amazingly collaborative human genome project—an awesome project that demonstrates the huge accomplishments that can come from scientists openly collaborating. Dr. Collins was the principle investigator of the first lab I joined at the very beginning of my academic research career. He is one of my science heroes, and I am really hoping that he becomes the next director of the NIH. With Collins at the helm, I have great confidence that the NIH will be a strong leader in funding and promoting Open Science and Science 2.0 innovations. The second post that caught my eye was by Jean-Claude Bradley discussing the possible necessity of science blogging. Jean-Claude is a huge proponent of Open Science and a leader in Open Notebook Science. Reading these posts made me wonder whether readers of the NextBio would like to know, “what is open science?”
- Jean-Claude Bradley
It wasn’t so long ago that the big discussion about scientists blogging was whether or not it would hurt your career. Granted, some the examples used involved personal content that would have been problematic on any platform. Still, many scientists chose to blog anonymously, even for the most uncontroversial scientific musings.
Recently I have noticed a change in the tone. The question doesn’t seem to be “Is blogging bad?” anymore but rather “Is blogging a waste of time?”. Often this involves the rather ironic situation of naysayers using a blog to express their opinion that blogging is a waste of time. There are many examples of this but a particularly controversial discussion took place on Nature Network recently.
- Jean-Claude Bradley
I have just finished reading the fascinating book “The Emperor of Scent” by Chandler Burr. It starts off describing the world of perfume with a focus on Luca Turin, a man with the unusual talent of being able to review perfumes with great eloquence, conjuring up beautiful metaphors of experiencing their scent.
The book then takes an unexpected turn into the description of Turin’s theory about the mechanism of olfaction. There is some truly interesting science there, such as Turin’s discovery of a binding site for NADPH and another for zinc on a protein thought to mediate smell. This supports his hypothesis that the protein functions as an electron tunneling spectroscope detecting differences in vibrational modes. Further evidence is provided by comparing the different smells of deuterated molecules like acetophenone and the similarity of the stench of boranes with thiols, which share similar IR spectral bands. This idea is at odds with the conventional view that molecular shape is responsible for the activity of odorants. (For a summary of Turin’s theory I would suggest watching his recent TED talk “The Science of Scent” and his Wikipedia entry).
- Hope Leman
It is 5:10 a.m. I am working on a netbook in a hotel room in San Francisco. I am attending the Web 2.0 Expo and covering it for the blog AltSearchEngines. While I am attending that event, I have been invited to a dinner sponsored by Microsoft Live Search. Yesterday I attended sessions about Web site monitoring and about how to build online social communities.
All of these activities tie into the world of Science 2.0 and Open Science. For example, the presenter on the online social communities asked what we would leave disappointed about if it were not addressed. I immediately shouted out, “FriendFeed!” because the Science 2.0 and Life Scientists rooms of FriendFeed are fascinating venues for those of us interested in how science is being conducted in the age of Web 2.0.