MSAcquisitionSimulator 1.0.2 – Data-dependent Acquisition Simulator for LC-MS Shotgun Proteomics

MSAcquisitionSimulator 1.0.2

:: DESCRIPTION

MSAcquisitionSimulator is a collection of three command-line tools that simulate data-dependent acquisition algorithms on in silico generated ground truth data of liquid chromatography-mass spectrometry proteomics experiments.

::DEVELOPER

Major Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MSAcquisitionSimulator

:: MORE INFORMATION

Citation

MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.
Goldfarb D, Wang W, Major MB.
Bioinformatics. 2015 Dec 17. pii: btv745.

SerialEM 3.7.11 – Electron Tomography Data & Image Acquisition

SerialEM 3.7.11

:: DESCRIPTION

SerialEM is a program to acquire tilt series for electron tomography on Tecnai and JEOL microscopes. It uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. It does not count on the microscope or the specimen being particularly well-behaved, so unless a prediction appears reliable, it falls back to measuring and adjusting defocus and/or specimen position when necessary. With this method, it achieves both the robustness of the older approach to tilt series acquisition (track and focus at every tilt) and the speed of the newer precalibration approach. A 2Kx2K, 1 degree tilt series can be acquired in about 45 minutes with a single-port readout camera or 20-25 minutes with a four-port readout camera.

::DEVELOPER

The Boulder Lab for 3D Electron Microscopy

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SerialEM

:: MORE INFORMATION

Citation:

Mastronarde, D.N. 2005.
Automated electron microscope tomography using robust prediction of specimen movements.
J. Struct. Biol.152:36-51.

FABIA 2.20.0 – Factor Analysis for Bicluster Acquisition

FABIA 2.20.0

:: DESCRIPTION

FABIA (Factor Analysis for Bicluster Acquisition) is a model-based technique for biclustering, that is clustering rows and columns simultaneously. FABIA is a multiplicative model that assumes realistic non-Gaussian signal distributions with heavy tails. FABIA utilizes well understood model selection techniques like variational approaches and applies the Bayesian framework. The generative framework allows FABIA to determine the information content of each bicluster to separate spurious biclusters from true biclusters. On 100 simulated data sets with known true, artificially implanted biclusters, FABIA clearly outperformed all 11 competitors. FABIA was tested on microarray data sets which known, biological verfified subclusters and performed on average best out of 11 biclustering approaches.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  FABIA

:: MORE INFORMATION

Citation

Sepp Hochreiter, Ulrich Bodenhofer, Martin Heusel, Andreas Mayr, Andreas Mitterecker, Adetayo Kasim, Tatsiana Khamiakova, Suzy Van Sanden, Dan Lin, Willem Talloen, Luc Bijnens, Hinrich W.H. Göhlmann, Ziv Shkedy, and Djork-Arné Clevert.
FABIA: Factor Analysis for Bicluster Acquisition,
Bioinformatics 2010, 26(12):1520-1527,

MAGMA 1.1 – Multiobjective Analyzer for Genetic Marker Acquisition

MAGMA 1.1

:: DESCRIPTION

MAGMA employs a multiobjective evolutionary algorithm to pick tag SNPs from a larger set of SNPs while balancing multiple objectives (e.g., cost and sensitivity).

::DEVELOPER

Family Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MAGMA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2003 Jul 23;4:30. Epub 2003 Jul 23.
Evolutionary algorithms for the selection of single nucleotide polymorphisms.
Hubley RM, Zitzler E, Roach JC.

XDIA – Extended Data-independent Acquisition

XDIA

:: DESCRIPTION

XDIA is a novel approach for data acquisition in shotgun proteomics.  XDIA combines high-resolution Orbitrap survey scans with multiplexed fragmentation data using data-independent acquisition with electron transfer dissociation, collision induced dissociation, or both.  The data are then post-processed by our new software, named XDIA Processor, which enables for protein identification.

::DEVELOPER

 Yates Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 XDIA

:: MORE INFORMATION

 

Citation

Paulo C. Carvalho, Xuemei Han, Tao Xu, Daniel Cociorva, Maria da Gloria Carvalho, Valmir C. Barbosa and John R. Yates III
XDIA: Improving on the label-free data-independent analysis
Bioinformatics (2010) 26 (6): 847-848.