From fd871f8dec0b1217b3d3b2be0a88875215612cd4 Mon Sep 17 00:00:00 2001 From: Stefan Badelt Date: Wed, 3 Jun 2020 11:44:19 -0700 Subject: [PATCH] added paper reference --- README.md | 5 ++--- case_studies/README.md | 3 ++- case_studies/Reactionrates.ipynb | 34 ++++++++++++++++---------------- peppercornenumerator/__init__.py | 2 +- setup.py | 2 +- 5 files changed, 23 insertions(+), 23 deletions(-) diff --git a/README.md b/README.md index 2587907..ffaa87d 100644 --- a/README.md +++ b/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)]: -[Badelt et al. (2020)]: +[Badelt et al. (2020)]: [example.pil]: [Seesaw Compiler]: diff --git a/case_studies/README.md b/case_studies/README.md index 4792ef7..9b81484 100644 --- a/case_studies/README.md +++ b/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)]: diff --git a/case_studies/Reactionrates.ipynb b/case_studies/Reactionrates.ipynb index 7c0d1e5..f58f951 100644 --- a/case_studies/Reactionrates.ipynb +++ b/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", diff --git a/peppercornenumerator/__init__.py b/peppercornenumerator/__init__.py index 801774e..af85b6c 100644 --- a/peppercornenumerator/__init__.py +++ b/peppercornenumerator/__init__.py @@ -2,7 +2,7 @@ # __init__.py # EnumeratorProject # -__version__ = "v0.8" +__version__ = "v0.9" import logging logging.getLogger(__name__).addHandler(logging.NullHandler()) diff --git a/setup.py b/setup.py index 3f4977a..ffcfc79 100755 --- a/setup.py +++ b/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",