case studies change

docs/_build_html/_sources/case_studies.rst.txt

@@ -45,7 +45,7 @@ CyTOF Data: Single Cell Immune Response to PMA Treatment
 
   Screenshot from the `Plasma_vs_PMA_Phosphrylation.ipynb`_ Jupyter notebook showing downsampled single cell CyTOF data (K-means downsampled from 220,000 single cells to 2,000 cell-clusters). Cell-clusters are shown as rows with cell-type categories (e.g. Natural Killer cells) and phosphorylations are shown as columns. See the interactive Jupyter notebook `Plasma_vs_PMA_Phosphrylation.ipynb`_ for more information.
 
-White blood cells are a key component of the immune system and kinase signaling is known to play an important role in immune cell function (see `Isakov and Altman 2013`_). Our collaborators in the `Giannarelli Lab`_ at the `Icahn School of Medicine Human Immune Monitoring Core`_ used Mass Cytometry, CyTOF (Fluidigm), to investigate the phosphorylation response of peripheral blood mononuclear cells (PBMC) immune cells exposed to PMA (phorbol 12-myristate 13-acetate), a tumor promoter and activator of protein kinase C (PKC). A total of 28 markers (18 surface markers and 10 phosphorylation markers) were measured in over 200,000 single cells. In the Jupyter notebook `Plasma_vs_PMA_Phosphrylation.ipynb`_ we semi-automatically identify cell types using surface markers and cluster cells based on phosphorylation to identify cell-type specific behavior at the phosphorylation level. See the `Plasma_vs_PMA_Phosphrylation.ipynb`_ Jupyter notebook for more information.
+White blood cells are a key component of the immune system and kinase signaling is known to play an important role in immune cell function (see `Isakov and Altman 2013`_). Our collaborators in the `Giannarelli Lab`_ and the `Icahn School of Medicine Human Immune Monitoring Core`_ used Mass Cytometry, CyTOF (Fluidigm), to investigate the phosphorylation response of peripheral blood mononuclear cells (PBMC) immune cells exposed to PMA (phorbol 12-myristate 13-acetate), a tumor promoter and activator of protein kinase C (PKC). A total of 28 markers (18 surface markers and 10 phosphorylation markers) were measured in over 200,000 single cells. In the Jupyter notebook `Plasma_vs_PMA_Phosphrylation.ipynb`_ we semi-automatically identify cell types using surface markers and cluster cells based on phosphorylation to identify cell-type specific behavior at the phosphorylation level. See the `Plasma_vs_PMA_Phosphrylation.ipynb`_ Jupyter notebook for more information.
 
 Large Network: Kinase Substrate Similarity Network
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docs/_build_html/case_studies.html

@@ -199,7 +199,7 @@ <h2>CyTOF Data: Single Cell Immune Response to PMA Treatment<a class="headerlink
 <a class="reference external image-reference" href="http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb"><img alt="CyTOF Screenshot" src="_images/CyTOF_screenshot.png" style="width: 450px;" /></a>
 <p class="caption"><span class="caption-text">Screenshot from the <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb">Plasma_vs_PMA_Phosphrylation.ipynb</a> Jupyter notebook showing downsampled single cell CyTOF data (K-means downsampled from 220,000 single cells to 2,000 cell-clusters). Cell-clusters are shown as rows with cell-type categories (e.g. Natural Killer cells) and phosphorylations are shown as columns. See the interactive Jupyter notebook <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb">Plasma_vs_PMA_Phosphrylation.ipynb</a> for more information.</span></p>
 </div>
-<p>White blood cells are a key component of the immune system and kinase signaling is known to play an important role in immune cell function (see <a class="reference external" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3831523/">Isakov and Altman 2013</a>). Our collaborators in the <a class="reference external" href="http://labs.icahn.mssm.edu/giannarellilab/">Giannarelli Lab</a> at the <a class="reference external" href="http://icahn.mssm.edu/research/portal/resources/deans-cores/human-immune-monitoring-core">Icahn School of Medicine Human Immune Monitoring Core</a> used Mass Cytometry, CyTOF (Fluidigm), to investigate the phosphorylation response of peripheral blood mononuclear cells (PBMC) immune cells exposed to PMA (phorbol 12-myristate 13-acetate), a tumor promoter and activator of protein kinase C (PKC). A total of 28 markers (18 surface markers and 10 phosphorylation markers) were measured in over 200,000 single cells. In the Jupyter notebook <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb">Plasma_vs_PMA_Phosphrylation.ipynb</a> we semi-automatically identify cell types using surface markers and cluster cells based on phosphorylation to identify cell-type specific behavior at the phosphorylation level. See the <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb">Plasma_vs_PMA_Phosphrylation.ipynb</a> Jupyter notebook for more information.</p>
+<p>White blood cells are a key component of the immune system and kinase signaling is known to play an important role in immune cell function (see <a class="reference external" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3831523/">Isakov and Altman 2013</a>). Our collaborators in the <a class="reference external" href="http://labs.icahn.mssm.edu/giannarellilab/">Giannarelli Lab</a> and the <a class="reference external" href="http://icahn.mssm.edu/research/portal/resources/deans-cores/human-immune-monitoring-core">Icahn School of Medicine Human Immune Monitoring Core</a> used Mass Cytometry, CyTOF (Fluidigm), to investigate the phosphorylation response of peripheral blood mononuclear cells (PBMC) immune cells exposed to PMA (phorbol 12-myristate 13-acetate), a tumor promoter and activator of protein kinase C (PKC). A total of 28 markers (18 surface markers and 10 phosphorylation markers) were measured in over 200,000 single cells. In the Jupyter notebook <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb">Plasma_vs_PMA_Phosphrylation.ipynb</a> we semi-automatically identify cell types using surface markers and cluster cells based on phosphorylation to identify cell-type specific behavior at the phosphorylation level. See the <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb">Plasma_vs_PMA_Phosphrylation.ipynb</a> Jupyter notebook for more information.</p>
 </div>
 <div class="section" id="large-network-kinase-substrate-similarity-network">
 <h2>Large Network: Kinase Substrate Similarity Network<a class="headerlink" href="#large-network-kinase-substrate-similarity-network" title="Permalink to this headline">¶</a></h2>

docs/case_studies.rst

@@ -45,7 +45,7 @@ CyTOF Data: Single Cell Immune Response to PMA Treatment
 
   Screenshot from the `Plasma_vs_PMA_Phosphrylation.ipynb`_ Jupyter notebook showing downsampled single cell CyTOF data (K-means downsampled from 220,000 single cells to 2,000 cell-clusters). Cell-clusters are shown as rows with cell-type categories (e.g. Natural Killer cells) and phosphorylations are shown as columns. See the interactive Jupyter notebook `Plasma_vs_PMA_Phosphrylation.ipynb`_ for more information.
 
-White blood cells are a key component of the immune system and kinase signaling is known to play an important role in immune cell function (see `Isakov and Altman 2013`_). Our collaborators in the `Giannarelli Lab`_ at the `Icahn School of Medicine Human Immune Monitoring Core`_ used Mass Cytometry, CyTOF (Fluidigm), to investigate the phosphorylation response of peripheral blood mononuclear cells (PBMC) immune cells exposed to PMA (phorbol 12-myristate 13-acetate), a tumor promoter and activator of protein kinase C (PKC). A total of 28 markers (18 surface markers and 10 phosphorylation markers) were measured in over 200,000 single cells. In the Jupyter notebook `Plasma_vs_PMA_Phosphrylation.ipynb`_ we semi-automatically identify cell types using surface markers and cluster cells based on phosphorylation to identify cell-type specific behavior at the phosphorylation level. See the `Plasma_vs_PMA_Phosphrylation.ipynb`_ Jupyter notebook for more information.
+White blood cells are a key component of the immune system and kinase signaling is known to play an important role in immune cell function (see `Isakov and Altman 2013`_). Our collaborators in the `Giannarelli Lab`_ and the `Icahn School of Medicine Human Immune Monitoring Core`_ used Mass Cytometry, CyTOF (Fluidigm), to investigate the phosphorylation response of peripheral blood mononuclear cells (PBMC) immune cells exposed to PMA (phorbol 12-myristate 13-acetate), a tumor promoter and activator of protein kinase C (PKC). A total of 28 markers (18 surface markers and 10 phosphorylation markers) were measured in over 200,000 single cells. In the Jupyter notebook `Plasma_vs_PMA_Phosphrylation.ipynb`_ we semi-automatically identify cell types using surface markers and cluster cells based on phosphorylation to identify cell-type specific behavior at the phosphorylation level. See the `Plasma_vs_PMA_Phosphrylation.ipynb`_ Jupyter notebook for more information.
 
 Large Network: Kinase Substrate Similarity Network
 ==================================================