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Simulation and Metadata Management


About me

scientific/academic code developer

run/manage simulations (code monkey)

an epic Pythonista (according to OSRC)

FiPy developer

interested in reproducible research, see


A declarative metadata standard

that you can use to tell a Linux VM how to download your data, execute your computational analysis, and spin up an interface to a literate computing environment with the analysis preloaded. Then we can provide buttons on scientific papers that say "run this analysis on Rackspace! or Amazon! Estimated cost: $25".

Automated integration tests for papers

where you provide the metadata to run your analysis while you're working on your paper and a service automatically pulls down your analysis source and data, runs it, and generates your figures for you to check. Then when the paper is ready to submit, the journal takes your metadata format and verifies it themselves, and passes it on to reviewers with a little "reproducible!" tick mark.

ideas by C. Titus Brown

Orthogonal Issues

Workflow Control

Scientific Development Process

Version Control

maintains history of workflow changes

but not workflow usage

already integrated into the scientific development process

Easy to use

$ git init
$ git add file.txt
$ git commit -m "add file.txt"
$ edit file.txt
$ git commit -am "edit file.txt"
$ git log
12e3c2618143 add file.txt
e00433e69a43 edit file.txt
$ git push github master

Manage Complexity

Event Control

provide a unique ID (SHA checksum) for every workflow execution

capture metadata, not data

not workflow control or version control

partial solution: Sumatra, a simulation management tool (not workflow)


doesn't change my workflow

records the metadata (not the data): parameters, environment, data location, time stamps, commit message, duration, data hash

generates unique ID for each simulation

Easy to use

$ smt init smt-demo
$ smt configure --executable=python
$ # python params.json
$ smt run --tag=demo --reason="create demo record" params.json wait=3
Record label for this run: '0c50797f1e3f'
No data produced.
Created Django record store using SQLite

Easy to use

$ smt list --long
Label            : 6c9c7cd2bbc2
Timestamp        : 2014-04-21 16:07:52.100838
Reason           : create demo record
Outcome          : 
Duration         : 3.26091217995
Repository       : GitRepository at /home/wd15/git/diffusion-worksho ...
Main_File        :
Version          : 08d04df6a9b561eb146d3a7461f763869fdc48a7
Script_Arguments : <parameters>
Executable       : Python (version: 2.7.6) at /home/wd15/anaconda/bi ...
Parameters       : {
                 :     "wait": 3
                 : }
Input_Data       : []
Launch_Mode      : serial
Output_Data      : []
User             : Daniel Wheeler <>
Tags             : demo
Repeats          : None

Web Interface

Sumatra + IPython + Pandas

high level data manipulation

quickly mix parameters, metadata and output data in a dataframe

save Sumatra records as HDF file

disseminate instantly using

Using Pandas

$ smt export
$ ipython
>>> import json, pandas
>>> with open('.smt/records_export.json') as f:
...     data = json.load(f)     
>>> df = pandas.DataFrame(data)
>>> custom_df = df[['label', 'duration', 'tags']]
>>> custom_df
   label         duration  tags
0  6c9c7cd2bbc2  3.260912  [demo]
1  db8610f0c51f  3.248754  [demo]
2  0fdaf12e0cb2  3.247553  [demo]
>>> custom_df.to_hdf('records.h5')

Using IPython

The Fantasy

cloud service for Sumatra

integrated with Github, Buildbot and a VM provider

sumatra-server 0.1.0 is out!



parallel demo: