[OpenMS] 2.0.0 RPMs released [F21 and F22]

OpenMS (follow this link for a quick start guide) is an openms2.0open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.

The release 2.0 is now ready to be installed from official Fedora repositories for testing.

Please, if you’re interested, install by YUM or DNF

# yum install openms-tools openms-tutorials openms-data openms openms-doc --enablerepo=updates-testing

and leave a positive(or)negative karma, otherwise write a comment in this post with your experience with it.

CHANGELOG

For a full list of resolved issues and changed tool parameters please refer to the CHANGELOG.

OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the build system. It introduces a considerable number of new features and bug fixes.
Furthermore, we removed the dependency to GSL and replaced the functionality using Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more permissive non-GPL (e.g., Apache or BSD) license.

File formats:
– mzQuantML support (experimental)
– mzIdentML support (experimental)
– mzTab support (experimental)
– Indexed mzML support
– Support for numpress encoding in mzML
– Major speed improvement in mzML / mzXML parsing (up to 4x for some setups)

TOPPView:
– Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1
– Improved “Tools” -> “Goto” dialog  – Improved display of m/z, RT, and intensity values 1D and 2D view

New tools:
– FeatureFinderIdentification — Detects features in MS1 data based on peptide identifications (TOPP)
– FeatureFinderMultiplex — Determination of peak ratios in LC-MS data (TOPP) for e.g. SILAC or Dimethyl labeling
– FidoAdapter — Runs the protein inference engine Fido (TOPP)
– LowMemPeakPickerHiRes — Finds mass spectrometric peaks in profile mass spectra (UTIL)
– LowMemPeakPickerHiRes_RandomAccess — Finds mass spectrometric peaks in profile mass spectra (UTIL)
– MRMTransitionGroupPicker (UTIL)
– MSGFPlusAdapter — MS/MS database search using MS-GF+ (TOPP)
– MetaboliteSpectralMatcher — Find potential HMDB ids within the given mass error window (UTIL)
– OpenSwathWorkflow — Complete workflow to run OpenSWATH (UTIL)
– PeakPickerIterative — Finds mass spectrometric peaks in profile mass spectra (UTIL)
– RTAnnotator — Annotates identification files that are missing the RT field (UTIL)
– SimpleSearchEngine — Annotates MS/MS spectra using SimpleSearchEngine (UTIL)
– TopPerc — Facilitate input to Percolator and reintegrate (UTIL)

Deprecated tools:
– DBExporter — Exports data from an OpenMS database to a file (TOPP)
– DBImporter — Imports data to an OpenMS database (TOPP)
– FeatureFinderRaw — Determination of peak ratios in LC-MS data (TOPP)
– SILACAnalyzer — Determination of peak ratios in LC-MS data (TOPP)

Status changes:
– PhosphoScoring (UTIL -> TOPP)
Tools with major changes:
– OpenSWATH now supports MS1 extraction and labelled workflows
– OpenSWATHWorkflow single binary (high performance integrated workflow)
– IsobaricAnalyzer now supports TMT 10-plex

General:
– Removed GSL dependencies  – Introduced low memory versions of various algorithms
– OpenMS now offers a single interface for different implementations to access mass spectrometric data
– in memory
– on disk with index
– cached on disc for fast access
as well as a chainable, low memory sequential processor of MS data (using a separate interface)
– pyOpenMS now supports python 3.x
– Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences

Third party software:
– Added Fido support
– Added MS-GF+ support

Changes to the Build System / Package System:
– Restructured repository layout and build system
– Added support for Travis CI
– Simplified pyOpenMS build system
– Support for Visual Studio 2013

[IceCat] 31.5.0

icecatIceCat 31.5.0 is packaged for Fedora 21 and Fedora 22.

Release notes:

* Updated to v31.5.0ESR
* Added build support for Windows, MacOS and Android
* Searchplugin instalation for mobile
* Make sure app.update and datareporting are disabled
* Updated html5-video-everywhere to 0.2.30
* Use prename instead of rename
* Adapt Spyblock for mobile
* Added patches to fix build bugs for Windows, MacOS and Android
* Enable LibreJs on mobile
* Updated aboutIcecat graphics
* Added android-images dir
* Fixed about:rights page content
* Added mobile branding files
* Added more fields to AddonsScraper.py
* Fake uname/arch no longer needed

Install it from updates repositories and navigate with this new release:

# dnf install icecat
Notice

IceCat user profile is located under $HOME/.gnu and not in $HOME/.mozilla; if you want preserve an old IceCat profile, you need to copy all profile data under $HOME/.mozilla/icecat in $HOME/.gnu/icecat.

mozilla-requestpolicy extension and IceCat

RequestPolicy is an extension for Mozilla browsers that requestpolicyincreases your browsing privacy, security, and speed by giving you control over cross-site requests.

Its development is continued by volunteers in a new website requetpolicycontinued.github.io; even though there are still some compatibility issues compared to the old 0.5 version, you can downgrade at any time.

What are cross-site requests?

Cross-site requests are requests that your browser is told to make by a website you are visiting to a completely different website. Though usually legitimate requests, they often result in advertising companies and other websites knowing your browsing habits, including specific pages you view throughout the day.

Cross-site requests are also used in attacks on users who are browsing the web. Among the attacks that cross-site requests are used in, they are particularly dangerous with Cross-Site Request Forgery (CSRF) attacks where your browser is told to make a request to another website and that other website thinks you (the person) meant to make the request.

Every informations and FAQs are reported on requetpolicycontinued.github.io.

Originally, RequestPolicy extension was provided in IceCat source archive, then replaced by SpyBlock, together with Https-Everywhere and LibreJS.

IceCat 31* packaging in Fedora excludes Https-Everywhere since it’s already available separately, while new mozilla-RequestPolicy (1.0) has just been packaged and diffused by Fedora repositories.

You can install it (F20,F21,EPEL6,EPEL7) with

yum install mozilla-requestpolicy