Free spectrum software for linux

libspectrum is a library designed to make the input and output of some ZX Spectrum emulator files slightly easier.

libspectrum is intended to be usable on Unix variants, Mac OS X and Win32. Currently, it is mainly (only?) used by Fuse, but other Spectrum emulator and utility authors are encouraged to use it.

Which formats does it support?

Snapshots:

read/write: .z80, .szx, .sna
read only: .zxs, .sp., .snp, +D snapshots

Tape images:

read/write: .tzx, .tap
read only: Warajevo .tap

Input recordings:

read/write: .rzx

Timex cartridges:

read only: .dck

Compressed files: reading of gzipped and bzipped files is transparently supported.

MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico.

SYNOPSIS

use MassSpec::ViewSpectrum::RealVsHypPeptide;
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
binmode GRAPHIC;

my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
130.1,132.1,147.7,157.1,158.1,159.1,169.1,171.1,175.1,187.1,229.1,246.2,258.1,
266.0,327.2,328.2,345.2,415.2,426.2,432.2,531.2,559.3,623.4,639.3,643.3,644.4,
645.0,647.5,686.4,687.4,689.4);
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
7.7,11.9,9.8,10.1,7.3,10.5,131.0,9.4,50.3,22.7,44.7,16.8,30.4,18.2,53.1,25.5,
15.7,7.7,14.0,46.8,38.4,7.3,11.5,8.7,7.3,8.7,7.3,24.8,194.2);
my $peptide = "RTSVAR";

my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);

my $output = $vs->plot();
print GRAPHIC $output;
close GRAPHIC;

MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.

Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.

Spectemu project is a 48k ZX Spectrum emulator.
Spectemu is a fast and nearly perfect emulation of the 48k ZX Spectrum computer. It can be run in an X11 window or on a Linux console. Features include sound output, tape emulation (with border stripes and sound), snapshot saving and loading, and an interactive keyboard picture.
It emulates the Z80 processor as well as the 48k Spectrums other hardware: keyboard, screen, sound, tape I/O. The emulation is very close to the real thing, but it is still quite fast (It was reported to be working well on a laptop with 486 at 25Mhz!).
On the other hand, the user interface is not the best. If you would like to see such features as Spectrum 128 or IF1 emulation, and dont mind the speed decrease, then have a look at xzx, another Spectrum emulator for UNIX. (Maybe sometime Spectemu will also support those.)
Main features:
- Quite fast
- X Support with MITSHM on a local display
- Console graphics support with Linux Svgalib
- Sound support (with Linux Open Sound System and SUN sound driver)
- Snapshot saving and loading (.z80 and .sna format)
- Tape emulation with .tap and .tzx files (I/O emulation with border striping and tape sound)
- Optional quick loading of tapefiles
- "Animated" keyboard picture NEW
- Configuration NEW

The Getfem++ project focuses on the development of a generic and efficient C++ library for finite element methods elementary computations. The goal is to provide a library allowing the computation of any elementary matrix (even for mixed finite element methods) on the largest class of methods and elements, and for arbitrary dimension (i.e. not only 2D and 3D problems).
Getfem offers a complete separation between integration methods (exact or approximated), geometric transformations (linear or not) and finite element methods of arbitrary degrees. It can really relieve a more integrated finite element code of technical difficulties of elementary computations.
Examples of available finite element method are : Pk on simplices in arbitrary degrees and dimensions, Qk on parallelepipeds, P1, P2 with bubble functions, Hermite elements, Argyris element, elements with hierarchic basis (for multigrid methods for instance), discontinuous Pk or Qk, XFem, vectorial elements (RT0, Nedelec) ...
The addition of a new finite element method is straightforward. Its description on the reference element must be provided (in most of the cases, this is the description of the basis functions, and nothing more). Extensions are provided for Hermite elements, piecewise polynomial, non-polynomial and vectorial elements, XFem.
The library also includes the usual tools for finite elements such as assembly procedures for classical PDEs, interpolation methods, computation of norms, mesh operations (including automatic refinement), boundary conditions, post-processing tools such as extraction of slices from a mesh ...
Getfem++ can be used to build very general finite elements codes, where the finite elements, integration methods, dimension of the meshes, are just some parameters that can be changed very easily, thus allowing a large spectrum of experimentations. Numerous examples are provided (see the screenshot section).
Getfem++ has no meshing capabilities (apart regular meshes), hence it is necessary to import meshes. Imports formats currently known by getfem are GiD , GmSH and emc2 mesh files. However, given a mesh, it is possible to refine it automatically.
Enhancements:
- The getfem and gmm header files have been moved into their respective subdirectories.
- The getfem interface (Python and MATLAB) is now included in the getfem distribution.
- Some C1 composite elements have been added (triangles and quadrilaterals).
- Support for Levelset functions has been improved.

Pagetool provides a CMS (content management system) that allows people with limited technical skills to contribute to a website.
What is Pagetool?
Pagetool is a program that allows people with limited technical skills to modify and contribute to an organizations web site via a web browser. There is no need for using an FTP program or for purchasing html editing programs like Dream Weaver or Go Live!. Furthermore, for basic site maintenance, no knowledge of HTML is necessary.
How Does it Work?
Pagetool stores all web pages in a database. To the average web user, it looks and acts like a typical web site. However, it you go to the special admin section and enter the correct username and password, you will be able to see a list of web pages on your site. By selecting a web page and clicking "edit" you will be able to change the content of that particular page.
Was Pagetool designed specifically for Nonprofits?
Media Jumpstart launched the Pagetool project (as a branch of myphpPagetool) with the express goal of making a web content management system appropriate for nonprofit organizations. As the project developed, however, it has attracted diverse developers who have been adapting it to work with for profit organizations, consultants, and universities, making it useful to a wide spectrum of organizations. The Pagetool project has since been taken over by Dave Guerin.
Enhancements:
- Added a link from the first setup page to the README_CGI.txt file for those that might need to do a manual install.
- Added an if !isset for $pt_action in pt_admin.inc. Maybe Pagetool 1.x will run with E_ALL error reporting someday :-)
- The new profile and edit profile admin screens now have valid html, plus a note about changing the colspan values for the header td and footer td thats required if theres no news bar.

InSilicoSpectro::InSilico::MSMSOutput is an object implementing common display/output methods for masses.

ATTRIBUTES

spectrum

A reference to a hash such as computed by MassCalculator::getFragmentMasses or an object of class MSMSTheoSpectrum.

expSpectrum

A reference to an experimental spectrum such as required by MassCalculator::matchClosest or an object of class ExpSpectrum. When this parameter is specified the constructor will assume that the hash spectrum contains data about the match with this experimental spectrum.

massIndex

The mass index in the experimental peak vectors, default 0. If expSpectrum parameter is an ExpSpectrum object this index is read from the object directly.

intensityIndex

The intensity index in the experimental peak vectors, default 1. If expSpectrum parameter is an ExpSpectrum object this index is read from the object directly.

tol

Relative mass error tolerance; this parameter is optional. When not specified, the matched masses found by the match algorithm are all preserved. When specified, the new tolerance is applied.

This parameter is mainly useful for match obtained via matchSpectrumClosest that does not apply any mass tolerance.

minTol

Absolute mass error, default value 0.2 Da. This parameter is used only in case tol parameter is specified, see above.

intSel

This parameter controls how the peak intensities are normalized, see function normalizeIntensities.

Parameter intSel is used provided expSpectrum was set.

prec

The number of digits after the decimal points for the masses. Default precision is 3 digits.

modifLvl

Controls how the modifications are highlighted in the vector splitPept defined below, see also function annotatePept.

cmp

This parameter is a reference to a comparison function used for sorting fragment names. If cmp is not set, the function cmpFragTypes is used instead.

Cora is a line fitting tool designed for emission line spectra with low count numbers.

Cora is an optional Gtk graphical user interface to the 7-part cora suite, which acts as a graphical front-end to cora_fit, and significantly facilitates the use of the latter.

It is a C-written program with graphical user interface. The program can also be run in IDL.

MassCalculator is a Perl module that implements common mass computations in mass spectrometry.

SYNOPSIS

use InSilicoSpectro::InSilico::MassCalculator;
InSilicoSpectro::InSilico::MassCalculator::init(insilicodef.xml);

MassCalculator Perl library is intended to support common mass spectrometry-related computations that must be routinely performed by bioinformaticians dealing with mass spectrometry data.

To accommodate as many as possible user requirements, we decided to both support a classical procedural programming model and an object oriented model. Per se MassCalculator is not designed as an object oriented code but we provide a series of elementary classes for modeling proteins, peptides, enzymes, etc. which MassCalculator is compatible with. Moreover, the latter classes are rather simple and neutral in their design such that they should fit, after further derivations eventually, a large range of code design.

We decided not to use Perl object oriented programming to stay with relatively naive and simple code and to allow everybody to decide how to include it in its own project. Nonetheless, MassCalculator is able to deal with Perl objects we provide additionally to represent protein sequences, peptides, enzymes, mass lists, and fragmentation spectra, see their respective documentations.
MassCalculator is released under the LGPL license (see source code).