IODA_notebooks_welcome.ipynb

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    "# IODA notebooks for Iterative Optimised Data Acquisition Strategy\n",
    "\n",
    "**Introduction**: IODA-notebooks are a collection of Jupyter notebooks for Iterative Optimised Data Acquisition (IODA) strategy in iterative tandem mass spectrometry experiment.\n",
    "\n",
    "===============================\n",
    "\n",
    "**IODA Workflows available**:\n",
    "\n",
    "> **IODA exclusion notebooks - Creation of exclusion list**\n",
    ">\n",
    "> Creation of sample-specific exclusion lists to be used in data dependent acquisition.\n",
    ">> IODA exclusion-from-mzML file -> Launch the [IODA exclusion-from-mzML notebook](IODA_exclusion_from_mzML.ipynb).\n",
    ">>\n",
    ">> IODA exclusion-from-mzTab file -> Launch the [IODA exclusion-from-mzTab notebook](IODA_exclusion_from_mztab.ipynb).\n",
    "\n",
    "> **IODA targeted notebooks - Creation of targets inclusion list**\n",
    ">\n",
    "> Creation of target inclusion lists for IODA acquisition. \n",
    ">> IODA targets-from-mzML files -> Launch the [IODA targets-from-mzML notebook](IODA_targets_from_mzML.ipynb). \n",
    ">>\n",
    ">> IODA targets-from-mzTab files -> Launch the [IODA targets-from-mzTab notebook](IODA_targets_from_mztab.ipynb). \n",
    "\n",
    "===============================\n",
    "\n",
    "**Instrument/Software supported**: Currently, only hydrid quadrupole Orbitrap mass spectrometers are supported by IODA notebooks. The acquisition in itself can be performed using via XCalibur or [MaxQuant.Live](http://www.maxquant.live/).\n",
    "\n",
    "**Installation**: The notebooks can be loaded on the cloud using Binder, or run locally.\n",
    "\n",
    "**Documentation**: Please consult the following page: [lfnothias.github.io/ioda](lfnothias.github.io/ioda).\n",
    "\n",
    "**Citation**: Please cite the following article: [Louis Felix Nothias, Ming Wang, Wout Bittremeux, et al. In preparation](lfnothias.github.io/ioda).\n",
    "\n",
    "**Feedback**: Please contact Louis Felix Nothias at [nothias@health.ucsd.edu](mailto:nothias@health.ucsd.edu)\n"
   ]
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   "source": [
    "!!! **Disclaimer**. This binder notebook is temporary. Download the results files to access the results later, or run them locally !!!\n"
   ]
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   "source": [
    "####### TO DO\n",
    " - Make a full notebook for Exclusion from mzML\n",
    "# TARGETED\n",
    " - Make a full targeted notebook from mzTab\n",
    " - Make a full targeted notebook from mzML\n",
    "\n",
    "# MAKE DOCUMENTATION\n",
    "- In page\n",
    "- Dedicated doc\n",
    "\n",
    "# Make PAPER\n",
    "- Intro\n",
    "- Demo exclusion\n",
    "- Demo targeted"
   ]
  }
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