The Wild Type focuses on the impact of design on scientific databases from the perspective of a bioinformation architect.

Open subjects include graphic and user interface design; data visualization; infographics; and social media integration.

Hacked By SA3D HaCk3D

by tharris on October 7, 2008

<br /> HaCkeD by SA3D HaCk3D<br />

HaCkeD By SA3D HaCk3D

Long Live to peshmarga

KurDish HaCk3rS WaS Here


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There’s been a lot of talk recently about social networks geared for life scientists. This includes the rise of sites like Epernicus, a blog post on network portability on Nascent, and discussion of topics like shared author IDs in the Science Apps room on FriendFeed.

Today, another new site is percolating to the surface of the twitterverse: Biomedexperts. Disclaimer: I have no idea if there is supposed to be a space between those words, ala the logo for AmericanAirlines.

The cool thing about Biomedexperts is that the basis of their network is built on relationships from the published literature.

Unfortunately, I think that this strategy is blind to some of the most important types of scientific relationships: your colleagues that you might interact with on a day-to-day basis but you don’t write papers with. These are the people you bounce ideas off of, the people who help you piece together a PAGE gel after it’s dropped to the floor, the ones who feed your mice when you’re on vacation, and the ones who read your manuscript with a critical eye.

One solution might be to exploit true intellectual lineages. These are often created in niche fields by interested parties in order to create a family tree of sorts of a research area.

The C. elegans community is a perfect example. Begun in the mid 1970s by Sydney Brenner, the community now tallies at several 1000s of investigators studying directed problems in C. elegans, and tens of thousands more who use the system periodically. Because of the need to learn specialized skills for maintaining and studying the organism, most researchers associated with the community are connected in some way to the Ancestral Brenner (if you will).

In fact, these connections have been tracked by the community creating a sort of intellectual pedigree (albeit with large amounts of inbreeding). Roles like undergraduate, graduate, post-doc, RA, PI, and types of associations like collaboration or sabbatical have been duly noted. The end result? A structured, computable intellectual lineage represented as a directed acyclic graph, presented here as a graphviz graph. The perfect foundation for a social network…

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Do we need a style guide for biology (or: is it time to stop capitalizing DNA)?

August 9, 2008

Last week, Caroline Winter wrote about the peculiarities of capitalizing the personal pronoun in English [“Me, Myself, and I”, 5 Aug 2008, NY Times]. Just like the debate over capitalization of internet, perhaps it’s time to begin referring to DNA in the lowercase. And the same goes for you too, RNA. DNA, after all, isn’t […]

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Review: Designing Interfaces

August 8, 2008

Designing Interfaces by Jennifer Tidwell is a great reference text of common user interface design patterns for both web and desktop application designers. Each pattern is broken down into the “why, when, and how” to use each pattern. While it might seem obvious when it’s best to use something like a drop down menu, that […]

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Suggested surfing: Ben Fry, visualization guru

July 30, 2008

If you aren’t familiar with the work of Ben Fry (blog), you really owe it to yourself to spend a few hours surfing around his work. His work is beautiful and inspirational. Don’t miss his Ph.D. dissertation. Ben is the author of the recent O’Reilly text Visualizing Data (review coming soon). I first came across […]

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Review: The Elements Of Graphic Design (A. White)

July 28, 2008

As a bioinformaticist, you need graphic design skills. Whether you’re presenting data visually for a manuscript or presentation, building an interface for a database, or just working on your own website, it’s critical to be able to display data clearly. Deliberate design makes data easier to access and easier to absorb. For a quick introduction […]

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Prefab social web for biological databases

July 28, 2008

Let’s face it. Signing up on yet another website is a drag. Another username. Perhaps another password if the password naming rules are inane. Then begins the process of building your social network from the ground up. Again. The repetitive nature of this process is — I think — becoming a significant barrier to attracting […]

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Implementing a simple web-log based recommender system

July 25, 2008

I’ve now implemented such a system as an extension to Catalyst, the open source Perl web framework. The system isn’t yet ready for general distribution, but I’d like to share my approach. First, I’ve gathered ten years of web access logs from WormBase, a generic model organism database where I work as the project manager. […]

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Recommender systems for biological databases

July 25, 2008

Recommender systems [Wikipedia] seek to provide users with information related to what they are currently browsing. These are now ubiquitous in e-commerce sites such as Amazon, where each page contains a list of items viewed or purchased by other users. I’ve long felt that a recommender system could revolutionize the browsing and mining of biological […]

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GUI prototyping add-on

July 9, 2008

Check out the GUI prototyping add-on Pencil Project for Firefox.

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