added paper reference

README.md

@@ -242,12 +242,11 @@ reaction [condensed      =        3e+06 /M/s ] S2 + R -> e51
         $ cat seesaw_ciruit.ssw | peppercorn --dry-run
 
 ## Version
-0.8
+0.9 -- Python 2.7 and Python 3 compatible, including SBML output standard.
 
 ## Authors
 Stefan Badelt, Casey Grun, Karthik V. Sarma, Brian Wolfe, Seung Woo Shin and Erik Winfree.
 
-[Grun et al. (2014)]: <https://arxiv.org/abs/1505.03738>
-[Badelt et al. (2020)]: <https://arxiv.org/abs/1505.03738>
+[Badelt et al. (2020)]: <https://doi.org/10.1098/rsif.2019.0866>
 [example.pil]: <https://github.com/DNA-and-Natural-Algorithms-Group/peppercornenumerator/blob/development/tests/examples/literature/kotani2017_F2.pil>
 [Seesaw Compiler]: <http://www.qianlab.caltech.edu/SeesawCompiler/AOtoSEESAW.php>

case_studies/README.md

@@ -1,5 +1,5 @@
 # Case study data 
-This directory contains the data used for the publication (in preparation):
+This directory contains the data used for the publication [Badelt et al. (2020)]:
 
 Badelt, Grun, Sarma, Wolfe, Shin, Winfree: 
 *A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures*
@@ -42,3 +42,4 @@ the analysis.
   * Qian2011.ipynb (Badelt et al. submitted, Figure 9)
   * Many_systems.ipynb (Badelt et al. submitted, Figure 10)
 
+[Badelt et al. (2020)]: <https://doi.org/10.1098/rsif.2019.0866>

case_studies/Reactionrates.ipynb

@@ -183,29 +183,29 @@
     "plt.tight_layout(w_pad = 3.5, h_pad=2.5)\n",
     "\n",
     "# add selected annotations\n",
-    "for x, y, tag, name in zip(tmpfig[\"Rate (experiment)\"], tmpfig[\"Rate (calculated)\"], tmpfig[\"(n, m)\"], tmpfig[\"Name\"]):\n",
-    "    if name == 'Zhang and Winfree (2009)\\n3-way strand displacement':\n",
-    "        #print(x,y,tag)\n",
-    "        if tag in [(1, 14),(2, 13),(3,12),(4,11),(7,8)]:\n",
-    "            g.axes[0].text(x+0.3, y-0.1, tag, horizontalalignment='left', size='small', color='black')\n",
-    "    elif name == 'Zhang and Winfree (2009)\\n3-way toehold exchange':\n",
-    "        #print(x,y,tag)\n",
-    "        if tag in [(1,1),(2,2),(3,3),(4,4),(5,5),(8,7)]:\n",
-    "            g.axes[1].text(x+0.3, y-0.1, tag, horizontalalignment='left', size='small', color='black')\n",
-    "    elif name == 'Dabby (2013)\\n4-way strand displacement':    \n",
-    "        #print(x,y,tag)\n",
-    "        if tag in [(2,2),(2,4),(2,6),(6,6),(6,4)]:\n",
-    "            g.axes[2].text(x+0.3, y-0.1, tag, horizontalalignment='left', size='small', color='black')\n",
-    "    else:\n",
-    "        print(x,y,tag,name)\n",
+    "#for x, y, tag, name in zip(tmpfig[\"Rate (experiment)\"], tmpfig[\"Rate (calculated)\"], tmpfig[\"(n, m)\"], tmpfig[\"Name\"]):\n",
+    "#    if name == 'Zhang and Winfree (2009)\\n3-way strand displacement':\n",
+    "#        #print(x,y,tag)\n",
+    "#        if tag in [(1, 14),(2, 13),(3,12),(4,11),(7,8)]:\n",
+    "#            g.axes[0].text(x+0.3, y-0.1, tag, horizontalalignment='left', size='small', color='black')\n",
+    "#    elif name == 'Zhang and Winfree (2009)\\n3-way toehold exchange':\n",
+    "#        #print(x,y,tag)\n",
+    "#        if tag in [(1,1),(2,2),(3,3),(4,4),(5,5),(8,7)]:\n",
+    "#            g.axes[1].text(x+0.3, y-0.1, tag, horizontalalignment='left', size='small', color='black')\n",
+    "#    elif name == 'Dabby (2013)\\n4-way strand displacement':    \n",
+    "#        #print(x,y,tag)\n",
+    "#        if tag in [(2,2),(2,4),(2,6),(6,6),(6,4)]:\n",
+    "#            g.axes[2].text(x+0.3, y-0.1, tag, horizontalalignment='left', size='small', color='black')\n",
+    "#    else:\n",
+    "#        print(x,y,tag,name)\n",
     "  \n",
     "(mi, ma)=(-2, 8)\n",
     "plt.xlim(-2.5, 8.5)\n",
     "plt.ylim(-2.5, 8.5)\n",
     "\n",
     "for ax in g.axes:\n",
-    "    ax.xaxis.set_major_formatter(plt.FuncFormatter(lambda x,y: \"$10^{{ {:.0f} }}$\".format(x)))\n",
-    "    ax.yaxis.set_major_formatter(plt.FuncFormatter(lambda x,y: \"$10^{{ {:.0f} }}$\".format(x)))\n",
+    "    ax.xaxis.set_major_formatter(plt.FuncFormatter(lambda x,y: \"$10^{{ {:.1f} }}$\".format(x)))\n",
+    "    ax.yaxis.set_major_formatter(plt.FuncFormatter(lambda x,y: \"$10^{{ {:.1f} }}$\".format(y)))\n",
     "\n",
     "    ax.plot([mi, ma], [mi, ma], linewidth=3, color='white', zorder=0)\n",
     "    ax.set(xlabel='Experimental rate constant [/M/s]')\n",

peppercornenumerator/__init__.py

@@ -2,7 +2,7 @@
 #  __init__.py
 #  EnumeratorProject
 #
-__version__ = "v0.8"
+__version__ = "v0.9"
 
 import logging
 logging.getLogger(__name__).addHandler(logging.NullHandler())

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='peppercornenumerator',
-    version='0.8',
+    version='0.9',
     description='Domain-level nucleic acid reaction enumerator',
     long_description=LONG_DESCRIPTION,
     long_description_content_type="text/markdown",