The A-Myth: running your lab as a business

<p>A-Myth stands for “The Academic Myth.” I want to challenge the conventional wisdom that research groups in academia should not be managed as businesses. It is tempting to take cover behind our non-profit status, our noble pursuit of knowledge, and other excuses to dismiss the idea that management methods used to run for-profit organizations do not apply to academic research groups or research institutes. Our metrics of success may not be the same but we will see that the methods to reach our own success may not be that different.</p> <p>This is a password-protected PowerPoint file. Open the file in read-only mode and Ignore the password prompt.</p

Fostering Transdisciplinary Science with Cyber-infrastructures

<p>Short presentation explaining the challenges and opportunities associated with transdisciplinary approaches to scientific problems. </p

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

This is the raw mRNA distributions used in the paper cited below. Data collected by David Ball

Measurement of transcriptional noise in the cell cycle regulatory network

<p>These are the raw images collected to analyze the noise affecting transcription in the control of the cell cycle in yeast. </p

A toolkit to implement 5S in a laboratory environment

<p>This file sent includes several files used in our group to implement the 5S methodology in a laboratory environment. We hope that this toolkit will help other people interested in using 5S in their own organization.</p> <p>The development of this resource was partly funded by NSF Award 1241328 "INSPIRE: Modeling and optimization of DNA manufacturing processes".  </p

Defining Domain-Specific DNA Programming Languages

<p>This is the slide deck of a presentation I gave at a workshop focused on "Advances in Molecular Programming and Computing: Toward Chemistry as a New Information Technology". This workshop took place in Denmark on May 2-4, 2013. </p> <p>The talk argues that different biotech applications call for the development of specific languages expressing specific design strategies. It illustrates the development of these domain-specific languages using the GenoCAD grammar editor. </p> <p>The PowerPoint presentation is password protected but it can be opened in Read-Only mode.</p

GenoCAD Grammar to design synthetic transcription factors in eukaryotes

<p>This file can be imported into GenoCAD for the design of synthetic transcription factors (sTFs) in eukaryotic cells. Knowledge derived from experimental evidence was captured in this grammar to guide the user to create designer transcription factors that should operate as intended. The grammar can be easily updated and refined as our experience with using sTFs in different contexts increases. This file is described extensively in the article referenced below. </p

GenoCAD Grammar to design Chlamydomonas reinhardtii expression vectors

<p>This is a grammar that can be imported into the web-based application GenoCAD to design expression vectors for expressing genes in the chloroplast of Chlamydomonas reinhardtii. Please refer to the publication linked to this entry for more information about this dataset. </p

GenoCAD Tutorials

<p>This tutorial includes two PowerPoint presentations developed by Mary Mangan from OpenHelix. Students should start with the Introduction prior to moving on to the Advanced tutorial. The slides decks include numerous comments that will help students go through the tutorials.</p> <p>In order to perform the hands on activities students need to download the GenoCAD Training Set. This dataset includes a list of parts and a grammar used as part of the GenoCAD Introductory tutorial.</p> <p>In order to import this data set in GenoCAD, proceed as follows:</p> <p>1- Log into GenoCAD, create an account if you don't already have one. </p> <p>2- Click on the Parts tab. </p> <p>3- Click on the Grammars tab. </p> <p>4- Click on the Add/Import Grammar button. </p> <p>5- Using the "choose file" button, select the grammar file (.genocad) and click on import grammar. </p> <p>6- Click on "use existing icon set" and click on "continue import".</p> <p>Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace.  </p> <p> </p> <p>The tutorial also includes a series of additional exercises that will be used to reinforce the concepts introduced in the tutorial. </p> <p>Please visit the GenoCAD page for videos of the tutotials. </p> <p> </p> <p> </p

Genetic Design Automation Worflows

<p>Comparison between the design automation loop in EDA and GDA. Projects follow parallel paths in both fields. Understanding what lessons from EDA can be applied for GDA is crucial to accelerating discovery in synthetic biology.</p