Big news at PLoS: today Mark Patterson announced on the PLoS blog that “As part of our ongoing article-level metrics program, we’re delighted to announce that all seven PLoS journals will now provide online usage data for published articles”. I downloaded the entire dataset and as a starter sorted it according to Combined Usage =… Continue reading Top 10 PLoS Articles based on online usage
Nature’s newest issue has a Quantitative genetics supplement with 3 free access pieces included out which I find this review the most interesting: Reverse engineering the genotype–phenotype map with natural genetic variation by Matthew V. Rockman. There’s a lot information to digest and many patterns to understand in this background field in order to approach… Continue reading Nature Insight: The complex trait of quantitative genetics
October 14, 2008 is the world’s first Open Access Day and OA itself means free online access to peer-reviewed research articles. Although we have other, slower methods, like personal homepages, emails to authors, institutional repositories to get the same article we were unable to get via closed access journals, OA is the internet-savvy solution that… Continue reading For your free information (FYFI): it’s Open Access Day!
Roni F. Zeiger, MD (watch his presentation), Google Health product manager, whose PubMed profile (if he really is the very same person) gives us a very strong reason why he was hired by Google for this job (he joined Google in 2006). The 38-year-old, who still sees patients some evenings and weekends at a nearby… Continue reading Meet Dr. Google Health: Roni Zeiger, right out of Stanford!
Not much happened since my announcement on Editing my doctoral thesis on stem cells in a blog: Why not?. I went to the U.S. first and started doing research instead of finishing my PhD education. But now I am back in this “getting a PhD” business as in January I passed the prerequisite comprehensive stem… Continue reading Warming up to write my thesis on the blog
The O’Reilly Emerging Technology Conference (ETech) is on and this year they had a growing number of biotech related sessions. Fellow SciFoo Campers like Hugh Rienhoff and Timo Hannay, Makers like Phil Torrone and Limor Fried, Brain Hackers like Ed Boyden are visiting and many more.
A partnership between the Journal of Visualized Experiments and big science publisher Wiley-Blackwell: the JoVE guys will give the technology, the art of making video experiments and Wiley provides the established network, audience on its Current Protocols site. I wonder what will be the access status of those videos: current JoVE videos are freely available,… Continue reading New JoVE helps old Wiley to publish video articles on Current Protocols
Jonathan Eisen is the new Academic Editor-in-Chief of PLoS Biology and wants to build a world in which Open Access and “top tier” can go hand-in-hand: So I accepted the invitation and became an Academic Editor. But I confess that I was not yet a true convert to OA or to PLoS Biology. So I… Continue reading ‘The horror of closed-access publishing’ according to Jonathan Eisen
Have you ever wanted to isolate subcellular components from molecules to organelles with the old but ever improving ultracentrifuge method but were unable to figure out a correct protocol as the basics were not that clear? To get an optimal protocol you have to take account the biological entity and pellet you want, the maximum… Continue reading Pelletology: the essence of ultracentrifugation in 14 slides
BioMed Search, the Google-like BioMedical Image Search Engine is alive after a long off period as it was relaunched about 1 month ago. Current informal science communication in the lab (say in lab meetings or in journal clubs) is centered around interpreting figures. BioMed Search catches somehow the essence of this communication with indexing the… Continue reading BioMed Search relaunched
My gmailbox says and I see no reason not to share it: The Open Aging Journal is an Open Access online journal, which publishes research articles, reviews and letters in all areas of aging science. The journal aims to provide the most complete and reliable source of information on current developments in the field. The… Continue reading The Open Aging Journal wants you to submit articles!
Similarly to the Edmonton Aging Symposium which reportedly “was a WORLD FIRST! in being streamed live onto the internet” (Kevin Perrott) amongst conferences, a selection of the presentations of the SENS3 conference are now available at the personal website of Richard Schueler. Richard is a big mouthed, cowboy hat geek with a serious life extension… Continue reading SENS3 conference videos online on a personal website
Positive, published scientific data form the tip of the iceberg of any scientific data produced in labs. As at least 90% (my guess) of all experiments are failed or lead to negative results, those data sets become “dark data“. But those dark data are as important for making science happen as positive data and this… Continue reading Freeing dark, negative research data is the next in open access science?
SciFoo is over, and I’ve just arrived back to New Orleans from SF. First of all: a big thanks for the organizers (Chris DiBona, Timo Hannay, Tim O’Reilly, Google, Nature, O’Reilly) and campers, it was really the highest end. Here is a quick SciFoo key terms summary (photos, detailed accounts later): “scientific data” One of… Continue reading SciFoo Camp, 2007: data (Google) publishing (Nature) geeks (O’Reilly)
Natureplex boss Timo Hannay published a landmark article draft on the web opportunities for the (more and more NPG boosted) scientific web. He highlighted 3 areas: audio-video content, databases (my emphasis), social software and summarized the science webspace with an artistic figure:
Science Direct-ly into Google by Peter Brantley, O’Reilly Radar: Elsevier has now undertaken to have the majority of its SD journals (those for which it holds or can obtain the copyrights) crawled and indexed by Google. Both Google and Google Scholar are slowly incorporating an increasing amount of this content, and these data will be… Continue reading Links from my reader/radar: Googlized Science Direct, Foo Camp, G Scholar as impact-o-meter
In my last “live” thesis post I said that the first steps of building a thesis are: figuring out a unifying concept behind all my experimental work and finding a proper thesis title. During my PhD work I’ve done various stem cell transplantations (local and systemic) into brain, heart, muscle tissues using different stem cell… Continue reading Choosing a proper title for the thesis: The physiologic role of stem cells…
Nature Precedings is “a free online service that enables researchers to rapidly share, discuss, and cite their early findings” launched on 18th June. I was really happy to be a beta tester, contribute and help to clear out some bugs. This line is from one of my mails 2 weeks before: “I find the idea… Continue reading Nature Precedings: a free preprint, poster and presentation sharing science service
me: Hi Bora, can you send me the Nature piece on the Blogging Anthology? I am not in the Institute and do not have subscription http://www.nature.com/nature/journal/v447/n7146/full/447779b.html Sent at 8:58 PM on Wednesday me: cheers 🙂 Bora: No problem. Thanks. me: wait that is some old stuff. Published online: 22 January 2007; | doi:10.1038/news070122-I’ve read that… Continue reading Uncensored gmail chat between 2 science bloggers on adult issues
No more waiting: Nature Reports Stem Cells (NRSC) launched today, and so finally there is a fully web native, scientifically high-end (naturally), freely accessible, all-in-one stem cell research hub site for everyone (especially for the researchers) to read, share, contribute and turn the acquired insights back into new experiments, policies, ethics, businesses and clinical trials.… Continue reading Nature Reports Stem Cells is live from now on…for stem cell enthusiasts
I found this exciting case in the book (yes, I am still reading those) of Lancet editor-in-chief Richard Horton called: Second Opinion: Doctors, Diseases and Decisions in Modern Medicine “Surgery is all about action, not reflection. But information is sometimes critical, even in the operating room. In 2002, surgeons in Australia were working frantically to… Continue reading Informational emergency in the operating room: does it count as a right?
Geoffrey P. Lomax, Zach W. Hall, Bernard Lo: Responsible Oversight of Human Stem Cell Research: The California Institute for Regenerative Medicine’s Medical and Ethical Standards Source: Plos blog, In the May issue of PLoS Medicine
From the Nautilus blog by Maxine Clarke: “Nature Reviews Neuroscience is the no. 1 monthly review journal in neuroscience, with an impact factor of 20.951. In May, online access to the entire issue is free.” I would like to offer these articles which could be of interest for stem cell biologists: Research Highlights Neurogenesis: Single… Continue reading Free Nature Reviews Neuroscience Issue in May
According to the organizers the Edmonton Aging Symposium “was a WORLD FIRST! in being streamed live onto the internet.” Now you can download where possible, the video, powerpoint and audio MP3 recordings of the streaming split up by speaker in alphabetical order. I think this is really webhistorical and good news for all open access… Continue reading Edmonton Aging Symposium: full video, audio and presentation access
Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer got interested in the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website. She shared with me her valuable thoughts and informations by mail, from which I now publish parts with the permission of Maxine Clarke… Continue reading Nature Publishing Editor on the idea of a public scientific multimedia site
In the last post on “supporting information” section I claimed that the problematic status of supporting information comes from the heterogeneity of its data, on the one hand genuine online multimedial files, on the other hand “paperlike” data. Big differences also occur concerning the importance of the data. The source of the heterogeneity is the… Continue reading Let’s make ‘supplementary’ peer-review scientific videos free and youtubish!
arXiv.org is the urform of open access scientific publishing since 1992, where “formal peer review is replaced by constant peer interest.” as Quinn Norton wrote. It is is THE preprint server for scientists in physics, maths, for instance, Grisha Perelman’s million dollar proof-sketch was first published here. But did you know that there are many… Continue reading Quantitative stem cell papers on arXiv.org
I republish here my “manifesto” like article on biotech DIY, which I wrote in April, 2006 on Newsvine in order to see the thoughts behind the placenta stem cell project. Would you like to sequence your genome in your garage? To grow your stem cells in the kitchen-lab? To hunt for point mutations just for… Continue reading What is bioDIY?
Oops, the folks at Nature Publishing Group are more and more watching us, the people of the second-generation Internet, you know the two point oh. Recently, the editor chief of Nature Medicine (impact factor 28.878 in 2005), Juan Carlos Lopez wrote and editorial and even a blog post concerning “what is the Web 2.0–driven scientific… Continue reading Nature Medicine 2.0 alarms by its editor in chief
Dear stem cell biologists and bioinformaticians: I’ve got a pretty serious question for you. How would you define and quantify the native (endogeneous, in-built) regenerative potential of a tissue/organ or more generally of a specially localized functional cell population in the human body? In the literature the term “regenerative potential” of a tissue is often… Continue reading How would you define the regenerative potential of a tissue/organ?
Journal of Visualized Experiments, or JoVE, the video focused science online journal was one of the most advanced and forward thinking newly launched website in 2006 in the field of life sciences. I am personally engaged in the topic of open source online protocol videos and JoVE is Pimm’s recurring theme. After the pioneer first… Continue reading Life Scientists: let us make video-articles for JoVE!
Check out the brand new BioMed Search, it is fantastic, currently over 1 million images have been indexed from peer-review journals in biomedical fields and more is on its way. BioMed Search has been created by Alex Ksikes, currently a Ph.D. candidate in Computer Science with focus in Computational Learning Theory at the University of… Continue reading The image of science: Google-like Biomedical Image Search Engine for pros
Thoughtful short piece on the new science video experiment site JoVE in The Scientist blog by Brendan Maher: “Videos like this could cut down troubleshooting time considerably. Moreover, there’s a great opportunity to create some new science stars. Who, after all, doesn’t have a running commentary going through their head as they run through the… Continue reading The Scientist on JoVE: Video makes the new science stars?
The first official issue of the new biological video protocol site JoVE or Journal of Visualized Experiments will be available today 11 pm EST, November 30, 2006. The graph shows November traffic in term of unique visitors, first 2.5 weeks mainly uploaders, authors, editors and editors’ friends used the page, from 17th there was a… Continue reading JoVE stats: blogosphere and Nature News traffic before official launch
Nature News has an article of the new Journal of Visual Experiments website, whereof Pimm had a story one week ago with the help of Moshe Pritsker, founder of the site. The title of the Nature News post: YouTube for test tubes, which sounds good really, but is problematic a little bit. In a way… Continue reading Nature News on JoVE: is JoVE really the YouTube for life scientists?
At last there is an almost perfect solution for life scientists to share video protocols and insider tricks to learn techniques and repeat experiments properly. Journal of Visualized Experiments (JoVE) is a newly founded and FREE online research journal that publishes video-articles on biological experiments (video-protocols). It is an independent project by 2 people, Moshe… Continue reading Biological Video Protocols on JoVE: Online Journal of Visualized Experiments
John Cumbers made the Drosophila CHiP protocol video. He is a graduate student at the Tatar lab in Brown University, USA. Below are his answers to the blogterview questions and through answer 5 you can take a fresh look at the bottom-up approach of synthetic biology.
Thanks to a new rapid publication policy you can download now 3 excellent articles from the November Issue of Tissue Engineering published by Mary Ann Liebert, Inc.: Ex Vivo Engineering of Living Tissues with Adult Stem Cells by Bonnie Barrilleaux, B.S., Donald G. Phinney, Darwin J. Prockop, and Kim O Connor. This is maybe the… Continue reading 3 free articles in the November Issue of Tissue Engineering