Ubuntu Science

"I’ve gone back to using another wonderful visualization package, PyMol. I find that it hits the sweet spot between easy setup of the scene I’d like and generating nice figures. The specific feature that I’ve come to rely on quite heavily is the built-in ray tracer. There are three available ray tracing modes in addition to the default, each of which has its uses. Mode 1 will place a black outline around your structure, which can help make the secondary structure elements visually distinct. Mode 2 is really interesting, in that it only renders the outline. I find this especially helpful if I want to show something in an overlay without obscuring what is behind it. Mode 3 produces “quantized” color in addition to the outline, giving your figure a very cartoonish appearance. I find that this one has to be used with care :) " - Mike Chelen from Bookmarklet

"Discussion of issues relating to the use of Debian for science research, including useful packages, particular problems faced by scientists using Debian, how to make Debian more useful to scientists, etc." - Mike Chelen from Bookmarklet

there are a number of useful software packages that have been integrated already, and debian makes a great foundation for science projects since it can run well on servers and desktops. it is also used as the basis for other popular derivatives like ubuntu - Mike Chelen

here are some of the packages currently available: http://blends.alioth.debian.org/science... - Mike Chelen

"Dear all, last year, Michael opened a discussion to have bibliographic information displayed in package summaries: http://lists.debian.org/msgid-s... In the discussion that followed, we talked about where to store this information, and in which format, since adding more content to the debian/control file is not an easy thing (it ‘costs’ a lot because it goes to pivotal files like the Packages.gz files on our mirrors). A four line summary is available here: http://wiki.debian.org/DebianS... This year, some progresses are being made. For the display, Andreas has modified the ‘Web sentinels’ so that they can display bibliographic informations. See http://debian-med.alioth.debian.org/tasks... for instance. But currently the limitation of the system is that the bibliographic information is in a quite remote location, in the Blends ‘tasks’ files. I am currently working on a new workflow which would help the... more... - Mike Chelen from Bookmarklet

"PhyLIS is a user-friendly, free linux distribution for phylogenetics. Install it and you have an instant phylogenetics workstation. No downloading packages or messing with compilers, no configuring software, no worrying about small differences between systems that mess up your scripts. Simply install, sit down, and work. PhyLIS started during a period when I was acquiring several new computers for a large phyloinformatic project and grew tired of installing general purpose linux distributions, and then having to spend an hour or two reconfiguring everything and adding software on each new computer. I began developing scripts that would do some of this work for me, eventually they became overly-complicated, and I still had to carry around thumbdrives full of software or needlessly re-download everything. Eventually it just became more desirable to have an operating system that was specifically geared towards doing phylogenetics. PhyLIS is based on Ubuntu linux, a widely used... more... - Mike Chelen from Bookmarklet

#debian-science on OFTC http://mibbit.com/#debian... - Mike Chelen

"This package contains function for reading and displaying PDB-files from the Brookhaven protein databank in Octave, a scientific computation software." - Mike Chelen from Bookmarklet

coming soon to a koala near you! - Mike Chelen

"Arguably the one producing the best (most accurate) results is Tesseract. It is a technology initially developed by HP Labs between 1985 and 1995, then they open-sourced it in 2005. Tesseract can recognize text in 7 different languages: English, German, French, Italian, Spanish, Brazilian Portuguese and Dutch. You can install more than one dictionaries if you need. It does not support layout analysis, so multi-column text, images, equations etc. should give you a garbled text output. Also, it only supports TIFF images as input." - Mike Chelen from Bookmarklet

"OCRopus(tm) is a state-of-the-art document analysis and Optical Character Recognition (OCR) system, featuring pluggable layout analysis, pluggable character recognition, statistical natural language modeling, and multi-lingual capabilities. The OCRopus engine is based on two research projects: a high-performance handwriting recognizer developed in the mid-90's and deployed by the US Census bureau, and novel high-performance layout analysis methods. OCRopus development is sponsored by Google and is initially intended for high-throughput, high-volume document conversion efforts. We expect that it will also be an excellent OCR system for many other applications." - Mike Chelen from Bookmarklet

"This package contains some ribosomal RNA BLAST databases distributed as part of the NCBI C Toolkit that are too large and specialized to include in ncbi-data. Specifically, it contains the databases Combined16SrRNA_2-12-2008, LSURef_93.fasta, and SSURef_93.fasta, along with an alias file to facilitate searching all three of them in conjunction with the 16SCore database included in ncbi-data." - Mike Chelen from Bookmarklet

"make deploying new Ubuntu servers both easier and more repeatable by relying on apt metapackages" - Mike Chelen from Bookmarklet

the guide for uploading to a #Launchpad #PPA is at https://help.launchpad.net/Packagi... - Mike Chelen