Posts Tagged Biology

3D Brain-wide Wiring Networks

The article from researchers in Taiwan recently came to my attention, presenting an OpenAccess database called “FlyCircuit“:

FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. For more details, please read the associated manuscript — “Three-dimensional reconstruction of brain-wide wiring networks inDrosophila at single-cell resolution”

So far, only the nervous system of the nematode C.elegans (ca. 300 cells) has been mapped comprehensively. In this study, 16,000 (out of approx. 100,000 total) single neurons were mapped to produce a virtual fly brain. The resulting map consists of 41 local processing units (LPUs), six hubs, and 58 tracts covering the whole Drosophila brain. “… the Drosophila brain is assembled from families of multiple LPUs and their interconnections. This provides an essential first step in the analysis of information processing within and between neurons in a complete brain.”

Hopefully this breakthrough will facilitate more open science in the neuro-anatomical research in future, at the moment FlyCircuit probably is the leading resource for scientists interested in higher-order brain-function.

See the Faculty of 1000 evaluations, dissents and comments for [Chiang AS et al. Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr Biol. 2011 Jan 11; 21(1):1-11; doi: 10.1016/j.cub.2010.11.056]. Faculty of 1000, 09 Sep 2011.

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Anatomy: interactive and three-dimensional

Visible Body built an interactive 3D model of the human anatomy now available for the iPad. They also have an interesting collection of celular and other animations / illustrations on their page:

Read the rest of this entry »

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In the bookstore …

During my studies, I made a habit of visiting the Cambridge University Press bookstore at least once a month. As a kind of wishlist, I noted potentially interesting new books – something I might continue in an open format here. Whenever the occasion and funding presented itself, I could draw from that list and get what seems most relevant and helpful. So far, reading on a tablet or screen does not quite have the same sensual appeal as a book for me quite yet – call me hopelessly old-fashioned. But of course, this being the 21st century, the advantage of carrying an entire electronic library with you in a tin-box that weighs less than your average textbook is a point that’s hard to argue about, especially in combination with advanced search and analysis tools. Nevertheless, here are some recent publications available in classical dead-tree format:

Systems Biology: Simulation of Dynamic Network States
Bernhard Ø. Palsson, University of California, San Diego

EMBOSS User’s Guide
Practical Bioinformatics
by Peter M. Rice, European Bioinformatics Institute, Hinxton
Alan J. Bleasby, European Bioinformatics Institute, Hinxton
Jon C. Ison, European Bioinformatics Institute, Hinxton

The Administrator’s Guide and Developer’s Guide are also available (by the very same authors in a different order).

The European Molecular Biology Open Software Suite (EMBOSS) is a well established, high quality package of open source software tools for molecular biology. It includes over 200 applications for molecular sequence analysis and general bioinformatics including sequence alignment, rapid database searching and sequence retrieval, motif identification and pattern analysis and much more.

The entire list of CUP titles in the section “Genomics, bioinformatics and systems biology” is here.

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Molecular Animations Galore

To continue with examples in communicating “what is it all good for”: the University of British Columbia’s former “iCapture Centre” (now James Hogg Research Centre) has done a great piece on linking Asthma treatment with the underlying genetic and molecular mechanisms. (Here is Part1 and Part2)

The animations were realised by Arkitek Studios and they made a science-demoReel available.

They did some impressive work for nature on RNAi:

This series of three animations was created for Nature Reviews Genetics in 2004, built originally to live on Nature’s site temporarily, perhaps a month or so.
Seven years later, with millions of hits, it has proven to be one of the most popular things Nature has ever had on its site.
Plans are in the works to revisit the piece, since much has been learned about RNAi in the interrim. Look for the new RNAi animation by the end of 2011.

Looking forward to it!
There is also a “Nature Education Scitable“, something on Cadherin,
Stem Cells – “What are they?”, GPCR proteins, and Large Scale Biology (Human Protein Index). Enjoy!

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Data vs. knowledge & insight

You’ve heard it before.
You’ve experienced it.
The data deluge is not really helping to generate knowledge, let alone novel insights,
or is it?
The mantra of data-mining is: just somewhere in the down there in the mountains of biological data the jewels are waiting to be found, you just have to keep digging. For myself, it never works quite that way.

I’m not getting into a discussion about hypothesis-driven vs. data driven science here and now, but this one is a breeze of different thinking. Although I don’t agree to it all, it’s worth watching:

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