UCSC, the institution that brought you the industry-standard genome browser, has now launched the UCSC Cancer Genomics Browser:

The browser is a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. This browser displays a whole-genome and pathway-oriented view of genome-wide experimental measurements for individual and sets of samples alongside their associated clinical information.

This site hosts the public UCSC Cancer Genomics Browser. The public site contains a rapidly growing body of publicly available cancer genomic data, including 12 published studies, datasets from the TCGA consortium, and others.

We encourage you to explore these data with our tools. The browser enables investigators to order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways, and user-edited collections of genes. Standard statistical tools are integrated to provide quantitative analysis of whole genomic data or any of its subsets.

I suspect that the Cancer Genomics Browser will provide an indispensable tool for biogerontologists who are seeking to explore the mechanistic connections between aging and cancer. I’m currently trying to think up an interesting way to use the service (and publicly available data) in my own work: e.g., tumors all have to undergo cellular senescence; would it be possible to find some fingerprint of senescence bypass mechanisms by looking at expression data from large numbers of tumors?


The new interactive Timeline of Discoveries in the Science of Aging (which I mentioned previously) is growing at a reasonable pace — it has roughly doubled in size since I first saw it, and now requires users to scroll down a bit.

I’ve added two articles and intend to do more:

Feel free to stop by and check those out.

If you feel that a major event in the history of biogerontology is missing from the timeline, I would encourage you to make an addition. Thanks to the site’s proprietor, Paul House, posting is relatively easy and entirely painless — though it’s not currently possible to go back and edit an entry yourself, so it probably makes sense to write and proofread your post before you start entering data into the form. If you know of a critical paper that’s not listed but don’t want to post yourself, you can still suggest it on the forum.

As I said before, I think this is a great idea and will be a fantastic educational and reference tool for the field, so I hope others will support the effort as well.

Lately I’ve been frequenting The Life Scientists room at the social networking/ microblogging/ forum site FriendFeed. I’ve been getting a lot out value out of it (I even used it to research an article I’m writing about social networking in science), so I wanted to mention it to other biologists who might be looking to take the plunge into the Web 2.0 world.

The room’s population is highly enriched in bioinformaticists, computational biologists and open-science advocates, so if those are interests of yours then you’ll find the discussions especially interesting. But if you’re not one of those things, don’t let that stop you; I’m hoping to see more experimental biologists join in. There are lot of conversations going on about new tools for science, but sometimes I feel like there aren’t enough experimentalists taking the opportunity to find out about the latest developments.

At the moment there’s no FF room devoted to biogerontology, but I suspect there’s not a big enough population of likely participants to give such a room momentum. Besides, we’re part of the larger edifice of biology; I’d rather talk with lots of different kinds of scientists than actively seek out isolation (and thereby risk becoming provincial).

(I’m also helping FriendFeed debug a feature that allows automated republishing of blog posts to twitter, so I thought it would be appropriate to make an entry about FriendFeed while I test the feature’s settings.)

Paul House has started a project that should be of wide interest to Ouroboros readers: a Timeline of Discoveries in the Science of Aging. His goal is to facilitate the creation of a record of the major events in the history of (bio-)gerontology, and publish it in a visual interactive form that grows in response to user input. Clicking on an individual event along the timeline expands it into a full article.

In Paul’s words (from a comment he made here earlier):

I have also been thinking about how to keep up with all the information, and struck on the idea of creating a timeline, that could maybe be a wiki(user driven).

My idea is to build a database of research on aging, keeping track of the date, name, institution, funding, technology, and tags. Then have the database/timeline filtered by any of those variables. I.E. Just show papers by one author…etc…

Anyway, I submit the link here if anyone would be willing to give feedback, of any kind, it would be much appreciated:



This technique could be of general utility in storing and displaying the historical record within a field — Paul has also initiated a timeline reflecting important milestones in the cell theory of life.

The idea is for the site to be interactive in multiple ways — not only in the sense that the timeline is a clickable object that expands in response to user behavior, but also in the sense that user-generated content can be incorporated into the object itself. It’s like a visual wiki.

So if you can think of a major event in the history of our field that belongs on the chart, visit the Science of Aging timeline and make an entry. (As soon as I post this I’m going to submit an entry about the Hayflick limit, which is the founding observation of my own field.)

I think this is a great idea, so I’m hoping that the community will support Paul’s effort.

PLoS ONE, one of the more radical open access journals, now has a blog: EveryONE. The inaugural post lays out the goals and raison d’etre for the effort, and answers such burning questions as…

Why a blog and why now? As of March 2009, PLoS ONE, the peer-reviewed open-access journal for all scientific and medical research, has published over 5,000 articles, representing the work of over 30,000 authors and co-authors, and receives over 160,000 unique visitors per month. That’s a good sized online community and we thought it was about time that you had a blog to call your own. This blog is for authors who have published with us and for users who haven’t and it contains something for everyone.

I was pleasantly surprised to see that Ouroboros is on the blogroll — possibly (OK, probably) because I’m on the editorial board, but it’s still nice. I figure that plugging their new blog is the least I could do:

They’re still on their first post but I’m sure there’s great stuff to come, so visit early and often!

The Institute for the Future has recently launched a future-forecasting forum called Signtific. The basic idea is that users will post short entries about significant upcoming changes (“signals”), combine their own signals with those of others to identify major shifts or disruptions that may arise in the future (“forecasts”), and discuss the ideas that emerge. It’s somewhere between a social networking site and a brainstorming session.

Activity is pretty low at the moment, though the site is still fairly new — so far no one has even initiated a conversation about biogerontology or related technologies, which clearly fall under the umbrella of significant future changes (hence my suspicion that Ouroboros readers would find this interesting) — but hopefully more people will join in as time goes on.

I’ve added a category to the right-hand column of the Ouroboros main page: “Links: Search”.

Recently I’ve been thinking a lot about ways to filter the literature. For scientists attempting to keep abreast of relevant knowledge, efficient search is necessary — though certainly not sufficient; even the best modern search tools either yield an unacceptably high false-positive rate (i.e., results that aren’t really of interest) or require a large investment of time and effort in order to tune searches for the needs of a specific user.

Search is improving, however, and I enjoy playing with the newest technologies. I’ve been a longtime adherent of HubMed, which is simply a better skin for PubMed. Lately I’ve been enjoying the intuitive interface of novo|seek, which allows the user to rapidly configure their search based on a group of related concepts, which the search engine delivers automatically based on the initial query terms.

So I’ve started a list of useful or otherwise noteworthy search tools. Check them out, share your thoughts, and let us know whether you’ve got a favorite that’s not already listed.

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