Jalview is a multiple alignment editor written in Java. It is used widely in a
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.
o Reads and writes alignments in a variety of formats
o Gaps can be inserted/deleted using the mouse.
o Group editing (insertion deletion of gaps in groups of sequences).
o Removal of gapped columns.
o Align sequences using Web Services (Clustal, Muscle...)
o Amino acid conservation analysis similar to that of AMAS.
o Alignment sorting options (by name, tree order, percent identity, group).
o UPGMA and NJ trees calculated and drawn based on percent identity distances.
o Sequence clustering using principal component analysis.
o Removal of redundant sequences.
o Smith Waterman pairwise alignment of selected sequences.
o Web based secondary structure prediction programs (JNet).
o User predefined or custom colour schemes to colour alignments or groups.
o Sequence feature retrieval and display on the alignment.
o Print your alignment with colours and annotations.
o Output alignments as HTML pages, images (PNG) or postscript (EPS).
If you use Jalview in your work, please quote this publication. Clamp, M., et
al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7
Apache Pig is a platform for analyzing large data sets that consists of a
high-level language for expressing data analysis programs, coupled with
infrastructure for evaluating these programs. The salient property of Pig
programs is that their structure is amenable to substantial parallelization,
which in turns enables them to handle very large data sets.
At the present time, Pig's infrastructure layer consists of a compiler that
produces sequences of Map-Reduce programs, for which large-scale parallel
implementations already exist (e.g., the Hadoop subproject). Pig's language
layer currently consists of a textual language called Pig Latin, which has
the following key properties:
-- Ease of programming. It is trivial to achieve parallel execution of simple,
"embarrassingly parallel" data analysis tasks. Complex tasks comprised of
multiple interrelated data transformations are explicitly encoded as data flow
sequences, making them easy to write, understand, and maintain.
-- Optimization opportunities. The way in which tasks are encoded permits the
system to optimize their execution automatically, allowing the user to focus
on semantics rather than efficiency.
-- Extensibility. Users can create their own functions to do special-purpose
processing.
Instead of a dry technical overview, I am going to explain the structure of this
module based on its history. I consult at a company that generates customer
leads primarily by having websites that attract people (e.g. lowering loan
values, selling cars, buying real estate, etc.). For some reason we get more
than our fair share of profane leads. For this reason I was told to write a
profanity checker.
For the data that I was dealing with, the profanity was most often in the email
address or in the first or last name, so I naively started filtering profanity
with a set of regexps for that sort of data. Note that both names and email
addresses are unlike what you are reading now: they are not whitespace-separated
text, but are instead labels.
Therefore full support for profanity checking should work in 2 entirely
different contexts: labels (email, names) and text (what you are reading).
Because open-source is driven by demand and I have no need for detecting
profanity in text, only label is implemented at the moment. And you know the
next sentence: "patches welcome" :)
The goal of the lensfun library is to provide an open source database of
photographic lenses and their characteristics. In the past there was an
effort in this direction (see http://www.epaperpress.com/ptlens/), but then
author decided to take the commercial route and the database froze at the
last public stage. This database was used as the basement on which lensfun
database grew, thanks to PTLens author which gave his permission for this,
while the code was totally rewritten from scratch (and the database was
converted to a totally new, XML-based format).
The lensfun library not only provides a way to read the lens database and
search for specific things in it, but also offers a set of algorithms for
correcting images based on detailed knowledge of lens properties and
calibration data. Right now lensfun is designed to correct distortion,
transversal (also known as lateral) chromatic aberrations, vignetting, and
colour contribution of the lens (e.g. when sometimes people says one lens
gives "yellowish" images and another, say, "bluish").
Ploticus is script-driven, which makes it suitable for automated, unattended
uses, or for applications that will be run again and again. Ploticus might be
your choice for stylistic reasons or just because it suits the problem or
application. In general, ploticus is good at making graphs like you would see
in newspapers and news magazines, business publications, journals for medical
and social sciences, and so on.
You can also use Ploticus in combination with standard desktop tools, e.g.
generate data displays using ploticus then import SVG or PNG into PowerPoint,
Word, etc.)
Ploticus is not a function or mathematical plotting package like gnuplot, nor
would it be a good choice for applications where mathematical formulas or
scientific notations are to be rendered as an integral part of the data
display. Ploticus is also not intended as a "marketing" graphics package. Its
goal is to display data crisply without extra decoration and distracting
"dingbats" that cloud the picture. Thus there is little support for 3-D
effects, gradient backgrounds, and so on.
FreeBSD note: the binary is referred to as 'pl' in the source files, but
is installed as 'ploticus' so as to avoid conflicts with other ports.
3[APA3A] tiny proxy 3Proxy (pronounce it as "Zaraza tiny proxy") is really
tiny cross-platform (Win32&Unix) proxy servers set. It includes HTTP proxy
with HTTPS and FTP support, SOCKSv4/SOCKSv4.5/SOCKSv5 proxy, POP3 proxy,
TCP and UDP portmappers. You can use every proxy as a standalone program
(socks, proxy, tcppm, udppm, pop3p) or use combined program (3proxy).
Combined proxy additionally supports features like access control,
bandwidth limiting, limiting daily/weekly/monthly traffic amount, proxy
chaining, log rotation, sylog and ODBC logging, etc. It's created to be
small, simple (I'd like to say secure - but it's just a beta) and yet
functional. It may be compiled with Visual C or gcc. Native Win32 version
included in archive and supports installation as NT/2K/XP service.
Currently 3proxy is tested to work under Windows 98/NT/2000/2003/XP,
FreeBSD/i386, Linux/i386, Linux/Alpha. See Release Notes and Changes for
features list.
3proxy is FreeWare. It can be used under terms of GNU/GPL or under its own
license (please read License Agreement).
For licensing or commercial support please e-mail to 3proxy@3proxy.ru
LIBSVM is an integrated software for support vector classification, (C-SVC,
nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation
(one-class SVM). It supports multi-class classification.
Since version 2.8, it implements an SMO-type algorithm proposed in this paper:
R.-E. Fan, P.-H. Chen, and C.-J. Lin. Working set selection using second order
information for training SVM. Journal of Machine Learning Research 6,
1889-1918, 2005. You can also find a pseudo code there.
Our goal is to help users from other fields to easily use SVM as a tool. LIBSVM
provides a simple interface where users can easily link it with their own
programs. Main features of LIBSVM include
* Different SVM formulations
* Efficient multi-class classification
* Cross validation for model selection
* Probability estimates
* Weighted SVM for unbalanced data
* Both C++ and Java sources
* GUI demonstrating SVM classification and regression
* Python, R (also Splus), MATLAB, Perl, Ruby, Weka, Common LISP and LabVIEW
interfaces. C# .NET code is available.
It's also included in some learning environments: YALE and PCP.
* Automatic model selection which can generate contour of cross valiation
accuracy.
Nux is a small, straightforward, and surprisingly effective open-source
extension of the XOM XML library. Nux is geared towards versatile embedded
integration and interchange, in particular for high-throughput server container
environments (e.g. large-scale Peer-to-Peer messaging network infrastructures
over high-bandwidth networks, scalable MOMs, etc). But its simplicity also
makes it useful for client side XML query/transformation workflow pipelines.
Features include:
- Seamless W3C XQuery support for XOM.
- Efficient and flexible pools and factories for XQueries, XSL Transforms, as
well as Builders that validate against various schema languages, including
W3C XML Schemas, DTDs, RELAX NG, Schematron, etc.
- For simple and complex continuous queries and/or transformations over very
large or infinitely long XML input, a convenient streaming path filter API
combines full XQuery support with straightforward filtering.
- Glue for integration with JAXB and for queries over ill-formed HTML.
- All this is rock-solid, dependable, well documented, and ships in a jar file
that weighs just 60 KB.
Advanced directory tree synchronisation tool
(c) 2014-2016 Thomas Khyn (c) 2003-2015 Anand B Pillai
Advanced directory tree synchronisation tool
based on Python robocopier by Anand B Pillai
Usage
From the command line:
dirsync <sourcedir> <targetdir> [options]
From python:
from dirsync import sync
sync(sourcedir, targetdir, action, **options)
LIRC is a package that allows you to decode and send infra-red signals
of many (but not all) commonly used remote controls.
The most important part of LIRC is the lircd daemon that will decode
IR signals received by the device drivers and provide the information
on a socket. It will also accept commands for IR signals to be sent if
the hardware supports this. The second daemon program called lircmd
will connect to lircd and translate the decoded IR signals to mouse
movements. You can e.g. configure X to use your remote control as an
input device.
The user space applications will allow you to control your computer
with your remote control. You can send X events to applications, start
programs and much more on just one button press. The possible
applications are obvious: Infra-red mouse, remote control for your TV
tuner card or CD-ROM, shutdown by remote, program your VCR and/or
satellite tuner with your computer, etc.