Archive for September, 2011

Free Science Books

A collection of free science books is available (in .pdf format) at INTECHopen – among them are the following ones on experimental / computational aspects of systems biology and on HMMs which might be of interest:

(thanks to Zana Kadric for sharing via the group “Systems Biology” at LinkedIn)

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Weekend Music Video

The future is not what it used to be :


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Exploring Big Data:” claims to be “The world’s largest community for exploring, sharing, creating, and promoting data visualizations.

Currently, there are over 3000 visualisations available on their site. Among my current favourites is this Infographics on Communication Through The Ages by Atlassian and this topological map of the internet, also available for download as desktop-wallpaper or poster here (at peer1hosting).

Well, data visualisation requires first of all that we get the appropriate data put together. With this all-important and often painful task pandas offers some help, pandas is “… becoming the most powerful and flexible open source data analysis / manipulation tool available in any language.” – they say. Sounds good, it’s based on numPy (scientific computing package for Python), will have to try it out at some point.

(thanks to Henning Stehr for hints on, pandas found via SchockWellenReiter)

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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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Nostalgia just isn’t what it used to be

To add to the category “yesterday’s views of tomorrow” – this “vision” from 1969 is in some aspects coming scarily close to what we call the ‘internet’ now:

Contrast this (rather narrow) “shopping/house/kids/surveillance/car/bills&taxes” outlook on the essentials of life with this view on the “computer network called ‘internet'” from 1993 Read the rest of this entry »

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Free web-based learning resource for life scientists

The EMBL-EBI just announced a beta version of Train online and will launch it publicly at the EMBO meeting over the weekend.

The PDBe: Quick tour and the UniProt: Quick tour seem like good primers on using these resources.

We’re delighted to announce that EMBL- EBI has launched the beta release of Train online.

What is Train online? Train online is a free, web-based learning resource for life scientists.

How can Train online help you? Train online helps you make the most of the huge amount of biological data that the EMBL-EBI makes publicly available for the research community. Using a combination of tutorials, guided examples, exercises and quizzes, Train online guides you towards becoming a confident user of open-access data resources. Current topics include data resources for genomics, functional genomics and proteomics. More will be added soon.

Who is Train online for? Train online is there for you to learn in your own time and at your own pace. You do not need previous experience in bioinformatics to benefit from our courses.

Want to know more? Visit Here you can access all our courses, as many times as you like, free of charge. We warmly invite you to register and sign up for Train online updates, which will alert you when we add new courses and features.

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Network-Sculpting in 3D

Not only the WWW, but also the roots of Linux date back about 20 years. (What the heck was going on back then?)
Happy birthday, little Penguin! It has waddled a long way, found many friends and has grown up considerably.

(see the Linux Foundation pages for more info, and I’ll spare you the historic details of my first install of a kernel with a version nr.<1.0). Besides that much of the internet rests on Linux, what’s that got to do with 3D and networks? Read the rest of this entry »

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