Scientific Software
===========================

We have been containerising scientific software to make it easy to
install, upgrade and deploy to DAaaS platform.

If you are developing any software that aims to be deployed into DAaaS
workspaces, packing it in `an
Apptainer <https://apptainer.org/docs/user/latest/>`__ is the fastest
way to get it deployed. Please get in touch if you need any guidance.

A full list of scientific software on DAaaS platform is in section of 
:doc:`software` below.

.. list-table:: 
    :widths: 50 30 10 10
    :header-rows: 1

    * - Software Name
      - Type
      - DAaaS
      - Ada
    * - `Amira-Avizo 3D <https://www.thermofisher.com/uk/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software/avizo-materials-science.html>`__
      - Apptainer & RPM
      - Yes
      - Yes
    * - `Anaconda3 <https://www.anaconda.com/>`__
      - Conda
      - Yes
      - Yes
    * - `ANTS2 <http://www.lip.pt/ants/ants2.html>`__
      - Apptainer
      - Yes
      - No
    * - `ASE <https://wiki.fysik.dtu.dk/ase/>`__
      - Virtualenv
      - Yes
      - No
    * - `Aten <https://www.projectaten.com/aten>`__
      - Apptainer
      - Yes
      - Yes
    * - `ATSAS <https://www.embl-hamburg.de/biosaxs/software.html>`__
      - Apptainer
      - Yes
      - No
    * - `Avogadro <https://avogadro.cc/>`__
      - Apptainer
      - Yes
      - Yes
    * - `Cambridge Structural Database System (CSD-System) <https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/>`__
      - RPM
      - Yes
      - No
    * - `CellProfiler <https://cellprofiler.org/>`__
      - Pip Package
      - Yes
      - No
    * - `Charmm <https://www.charmm.org/>`__
      - RPM
      - Yes
      - No
    * - `Chimera <http://www.cgl.ucsf.edu/chimera/index.html>`__
      - RPM
      - Yes
      - No
    * - `Chimerax <https://www.cgl.ucsf.edu/chimerax/>`__
      - Apptainer
      - Yes
      - No
    * - `CrystalPlan <https://github.com/samueljackson92/CrystalPlan>`__
      - RPM
      - Yes
      - No
    * - `CSD-CrossMiner <https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/CSD-CrossMiner/>`__
      - RPM
      - Yes
      - No
    * - `CTFFIND <https://grigoriefflab.umassmed.edu/ctffind4>`__
      - RPM
      - Yes
      - No
    * - `DAVE <https://www.ncnr.nist.gov/dave/index.html>`__
      - Apptainer
      - Yes
      - No
    * - `DiffPy-CMI <https://www.diffpy.org/index.html>`__
      - Conda
      - Yes
      - No
    * - `DifMag <https://forge.epn-campus.eu/projects/difmag>`__
      - RPM
      - Yes
      - No
    * - `Dissolve <https://www.projectdissolve.com/>`__
      - Apptainer
      - Yes
      - No
    * - `DL_Poly <https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx>`__
      - RPM
      - Yes
      - No
    * - `Doppio <https://github.com/NagariaHussain/doppio>`__
      - RPM
      - Yes
      - Yes
    * - `EC-CLEM <https://github.com/anrcrocoval/ec-clem>`__
      - RPM
      - Yes
      - No
    * - `Emacs <https://www.gnu.org/savannah-checkouts/gnu/emacs/emacs.html>`__
      - Linux Package
      - No
      - Yes
    * - `epac_ct <https://www.clf.stfc.ac.uk/Pages/EPAC-introduction-page.aspx>`__
      - Conda
      - Yes
      - No
    * - `EPSR <https://www.isis.stfc.ac.uk/Pages/Empirical-Potential-Structure-Refinement.aspx>`__
      - Apptainer & RPM
      - Yes
      - No
    * - `Euphonic <https://euphonic.readthedocs.io/en/latest/>`__
      - Virtualenv
      - Yes
      - No
    * - `Fiji <https://fiji.sc/>`__
      - RPM & Apptainer
      - Yes
      - Yes
    * - `FullProf <https://www.ill.eu/sites/fullprof/index.html>`__
      - Apptainer
      - Yes
      - No
    * - `Geant4 <https://geant4.web.cern.ch/>`__
      - Apptainer
      - Yes
      - No
    * - `GenX <http://genx.sf.net>`__
      - Apptainer
      - Yes
      - Yes
    * - `Grace <https://plasma-gate.weizmann.ac.il/Grace/>`__
      - RPM
      - Yes
      - No
    * - `GROMACS <http://www.gromacs.org/>`__
      - Apptainer
      - Yes
      - No
    * - `GSAS-II <https://subversion.xray.aps.anl.gov/trac/pyGSAS>`__
      - Apptainer
      - Yes
      - Yes
    * - `GSAS(old) <https://subversion.xray.aps.anl.gov/trac/EXPGUI>`__
      - Apptainer
      - Yes
      - No
    * - `GudPy <https://github.com/disorderedmaterials/GudPy>`__
      - Apptainer
      - Yes
      - No
    * - `Gudrun <https://www.isis.stfc.ac.uk/Pages/Gudrun.aspx>`__
      - Apptainer & RPM
      - Yes
      - No
    * - `Herbert <https://pace-neutrons.github.io/Horace/v3.6.2/manual/Herbert.html>`__
      - Matlab Package
      - Yes
      - No
    * - `Horace <http://horace.isis.rl.ac.uk/Main_Page>`__
      - Matlab Package
      - Yes
      - No
    * - `Horace-Euphonic Interface <https://github.com/pace-neutrons/horace-euphonic-interface>`__
      - Matlab Package
      - Yes
      - No
    * - `Huygens <https://svi.nl/Huygens-Software>`__
      - RPM & Apptainer
      - Yes
      - No
    * - `Icy <http://icy.bioimageanalysis.org/>`__
      - RPM
      - Yes
      - Yes
    * - `IgorPro <https://www.wavemetrics.com/products/igorpro>`__
      - Yum Package
      - Yes
      - No
    * - `Ilastik <https://www.ilastik.org/>`__
      - Application
      - Yes
      - Yes
    * - `ImageJ <https://imagej.net/ij/index.html>`__
      - Application
      - No
      - Yes
    * - `Jana2006 <http://jana.fzu.cz/>`__
      - Yum Package
      - Yes
      - No
    * - `Jmol <http://jmol.sourceforge.net/>`__
      - Apptainer
      - Yes
      - Yes
    * - `JournalViewer <https://epubs.stfc.ac.uk/manifestation/27193192/RAL-TR-2016-002.pdf>`__
      - Apptainer
      - No
      - Yes
    * - `Jupyter <https://jupyter.org/>`__
      - Pip Package
      - Yes
      - Yes
    * - `Krita <https://krita.org/en/>`__
      - Ubuntu Package
      - No
      - Yes
    * - `LabVIEW <https://www.ni.com/en-gb/shop/labview.html>`__
      - RPM
      - Yes
      - No
    * - `LAMMPS <https://www.lammps.org>`__
      - Apptainer
      - Yes
      - No
    * - `Lmfit <https://lmfit.github.io/lmfit-py/>`__
      - Pip Package
      - Yes
      - No
    * - `Mantid <https://www.mantidproject.org/>`__
      - Conda
      - Yes
      - No
    * - `Mantid Imaging <https://mantidproject.github.io/mantidimaging/>`__
      - Conda
      - Yes
      - No
    * - `Materials Studio <https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-materials-studio/>`__
      - Apptainer
      - Yes
      - No
    * - `Mathematica <https://www.wolfram.com/mathematica/>`__
      - RPM
      - Yes
      - No
    * - `Matlab <https://uk.mathworks.com/products/matlab.html>`__
      - RPM
      - Yes
      - No
    * - `McSAS <https://bitbucket.org/pkwasniew/mcsas/src/master/>`__
      - Yum Package
      - Yes
      - No
    * - `McStas <http://www.mcstas.org/>`__
      - Apptainer & RPM
      - Yes
      - No
    * - `McStas RPM <http://www.mcstas.org/>`__
      - RPM
      - Yes
      - No
    * - `McXtrace <https://www.mcxtrace.org/>`__
      - Apptainer
      - Yes
      - No
    * - `MDANSE <https://mdanse.org/>`__
      - Apptainer
      - Yes
      - Yes
    * - `MDMC <http://mdmcproject.org/>`__
      - Python Package
      - Yes
      - No
    * - `ModelAngelo <https://github.com/3dem/model-angelo>`__
      - Conda
      - Yes
      - No
    * - `Mslice <http://mslice.isis.rl.ac.uk/>`__
      - Matlab Package
      - Yes
      - No
    * - `MSMM <??>`__
      - Octopus Package
      - Yes
      - No
    * - `MTEX <https://mtex-toolbox.github.io/index>`__
      - RPM
      - Yes
      - No
    * - `Mumax3 <http://mumax.github.io/>`__
      - Yum Package
      - Yes
      - No
    * - `MuSRFit <http://lmu.web.psi.ch/musrfit/technical/>`__
      - Apptainer
      - Yes
      - No
    * - `MuSRSim <https://www.psi.ch/en/lmu/geant4-simulations>`__
      - Apptainer
      - Yes
      - No
    * - `NAMD <https://www.ks.uiuc.edu/Research/namd/>`__
      - Yum Package
      - Yes
      - No
    * - `Napari <https://napari.org/stable/index.html>`__
      - Pip Package
      - No
      - Yes
    * - `NSXTool <https://code.ill.fr/scientific-software/nsxtool>`__
      - Yum Package
      - Yes
      - No
    * - `OCLIMAX <https://sites.google.com/site/ornliceman/oclimax>`__
      - Apptainer
      - Yes
      - No
    * - `Octave <https://octave.org/>`__
      - Apptainer
      - Yes
      - No
    * - `Openfoam <https://www.openfoam.com/>`__
      - Apptainer
      - Yes
      - No
    * - `OpenHKL <https://neutron-simlab.iffgit.fz-juelich.de/openhkl/about.html>`__
      - Apptainer
      - Yes
      - No
    * - `OpenMC <https://docs.openmc.org/en/stable/>`__
      - Conda
      - Yes
      - No
    * - `Packmol <https://m3g.github.io/packmol/>`__
      - Apptainer
      - Yes
      - No
    * - `Paraview <https://www.paraview.org/>`__
      - Desktop Application
      - No
      - Yes
    * - `Phenix <https://phenix-online.org/>`__
      - RPM
      - Yes
      - No
    * - `Phonopy <https://phonopy.github.io/phonopy/>`__
      - Conda
      - Yes
      - No
    * - `ptypy <https://ptycho.github.io/ptypy/>`__
      - Yum Package
      - Yes
      - No
    * - `PyMuonSuite <https://github.com/muon-spectroscopy-computational-project/pymuon-suite>`__
      - Pip Package
      - Yes
      - No
    * - `Quantum Espresso <https://www.quantum-espresso.org/>`__
      - Apptainer
      - Yes
      - No
    * - `R <https://www.r-project.org/>`__
      - Yum Package
      - Yes
      - Yes
    * - `Radia <https://www.esrf.eu/Accelerators/Groups/InsertionDevices/Software/Radia/>`__
      - Yum Package
      - Yes
      - No
    * - `RasCAL <https://github.com/arwelHughes/RasCAL_2019>`__
      - Matlab Based
      - Yes
      - No
    * - `Refl1D <https://refl1d.readthedocs.io/en/latest/index.html>`__
      - Pip Package
      - Yes
      - No
    * - `RefNX <https://refnx.readthedocs.io/en/latest/>`__
      - Conda & Mamba Package
      - Yes
      - No
    * - `RMCProfile <http://www.rmcprofile.org/Main_Page>`__
      - Apptainer & RPM
      - Yes
      - No
    * - `RNAView <https://github.com/rcsb/RNAView>`__
      - Apptainer & RPM
      - Yes
      - No
    * - `RStudio <https://posit.co/products/open-source/rstudio/>`__
      - IDE
      - No
      - Yes
    * - `SASfit <https://www.psi.ch/en/sinq/sansi/sasfit>`__
      - Apptainer
      - Yes
      - No
    * - `SasView <https://www.sasview.org>`__
      - Yum Package
      - Yes
      - No
    * - `spinW <https://spinw.org/>`__
      - Matlab Library
      - Yes
      - No
    * - `Spyder <https://www.spyder-ide.org/>`__
      - IDE
      - Yes
      - Yes
    * - `SRIM <http://srim.org/>`__
      - RPM
      - Yes
      - No
    * - `SScanSS 2 <https://isisneutronmuon.github.io/SScanSS-2/>`__
      - Apptainer & RPM
      - Yes
      - No
    * - `Sunny <https://github.com/SunnySuite/Sunny.jl#readme>`__
      - Julia Package
      - Yes
      - No
    * - `Tensorboard <https://www.tensorflow.org/tensorboard>`__
      - Pip Package
      - Yes
      - Yes
    * - `VESTA <https://jp-minerals.org/vesta/en/>`__
      - Apptainer
      - Yes
      - Yes
    * - `VisIt <https://visit-dav.github.io/visit-website/>`__
      - Apptainer
      - Yes
      - Yes
    * - `VMD <https://www.ks.uiuc.edu/Research/vmd/>`__
      - Yum Package
      - Yes
      - No
    * - `VS Code <https://code.visualstudio.com/>`__
      - IDE
      - Yes
      - Yes
    * - `WiMDA <http://shadow.nd.rl.ac.uk/wimda/>`__
      - Yum Package
      - Yes
      - No
    * - `Zim <https://zim-wiki.org/>`__
      - Ubuntu Package & Apptainer
      - Yes
      - Yes