MurrayRM:Software notes: Difference between revisions
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== Synthetic biology software == | == Synthetic biology software == | ||
== Lab software == | |||
This is some of the software that I have used for supporting experimental work in the lab. | |||
* Notebook - Software for creating lab notebooks. Has good support for time-tagging, importing images, etc. Mainly useful for things you would put in a lab notebook (as opposed to other types of notes). | |||
* aPE - Plasmid editing software. I use this for viewing and annotating sequencies | |||
== General purpose software == | |||
* Evernote - I use this for tacking notes on various topics. Uploads notes to the cloud and does handwriting recognition on scanned notes and blackboard photos. | |||
* Papers (Mac) - this is what I used to keep track of all of my technical papers. | |||
* TimeLog (Mac) - I use this to track my time on different tasks, including consulting. | |||
* Things (Mac) - keep track of action items and tasks that I need to remember to do | |||
== Unused software == | |||
I've downloaded quite a few software packages that I don't seem to use very much (yet). | |||
* EnzymeX - Software from mekentosj for working with restriction enzymes (I don't do this all that often and have used NEBcutter for this purpose) | |||
* LabAssistant - Software from mekentosj for planning out experiments. I've found it easier to just write out what I want to do in my lab notebook (printed or electronic) | |||
Revision as of 11:38, 6 March 2010
This page has some notes on different software packages that I am looking using or considering using. Mainly just a place to collect information and links for me and my collaborators.
General purpose software
Mathematical analysis
- MATLAB
- SciPy
- R
Systems biology software
Modeling and analysis
- CellDesigner
- COPASI
- Simulac
- StochKit
Flow cytometry (FCM)
- FlowJo - FlowJo is a commercial program for reading and displaying FCM data.
- Weasel - Weasel is an open source tool for reading and displaying FCM data.
- Bioconductor/flow (R) - Bioconductor is a suite of software tools for working with bioinformatics data. The flow package is a set of tools that are designed to read, process and view FCM data. The iFlow package provides a GUI style interface to data that is intended for exploration.
Synthetic biology software
Lab software
This is some of the software that I have used for supporting experimental work in the lab.
- Notebook - Software for creating lab notebooks. Has good support for time-tagging, importing images, etc. Mainly useful for things you would put in a lab notebook (as opposed to other types of notes).
- aPE - Plasmid editing software. I use this for viewing and annotating sequencies
General purpose software
- Evernote - I use this for tacking notes on various topics. Uploads notes to the cloud and does handwriting recognition on scanned notes and blackboard photos.
- Papers (Mac) - this is what I used to keep track of all of my technical papers.
- TimeLog (Mac) - I use this to track my time on different tasks, including consulting.
- Things (Mac) - keep track of action items and tasks that I need to remember to do
Unused software
I've downloaded quite a few software packages that I don't seem to use very much (yet).
- EnzymeX - Software from mekentosj for working with restriction enzymes (I don't do this all that often and have used NEBcutter for this purpose)
- LabAssistant - Software from mekentosj for planning out experiments. I've found it easier to just write out what I want to do in my lab notebook (printed or electronic)
