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Roadmap: Flotilla

(Format copied from https://github.com/ipython/ipython/wiki/Roadmap:-IPython)

This document describes the goals, vision and direction of the Flotilla project. Flotilla is a biological data analysis toolkit aiming to ease integration of various datatypes and datasets together to solve biological questions, and put the biological interpretation of computational results into the hands of experimental biologists, and leave the algorithms and development to the computational biologists. Additionally, we see the use of the IPython notebook with its plotting and interactivity as a "gateway drug" for biologists to learn to code and invent their own analyses. Currently, Flotilla is focused on single-cell RNA-Seq analyses.

As in the IPython roadmap, we will indicate tasks by:

  • Difficulty: Easy (E), Medium (M), Hard (H)
  • Priority: 0 (most important), 1, 2, 3 (least important)
  • Developer leading this task (doesn't have to be sole contributor, but this is the point person to coordinate with if you want to contribute to one of these tasks)

Eventually, we would like Flotilla to easily hook into and be hosted on an Amazon EC2 server to perform computations and download memory-intensive databases.

Overview of 2014

Our work is being funded by the NumFOCUS foundation for July-December 2014. With their support, we aim to release a stable, working product to users early on, and from this release gain feature requests and bug reports for edge cases we haven't thought of.

Summer 2014

Currently, this project is private. Before we open this publicly, we need to fix the following bugs:

  • "Not" sample subset groups (e.g. "not neuron"): #54
  • Weird PC loadings: #56

We plan to release a working version before August 15th, 2014. In addition to current functionality, this version ("0.2?") will have the following spec:

  • (E, 0) Naming issues. experiment_design data is apparently uninterpretable. Could go with sample_metadata or phenotype_data (as in BioconductoR) instead.
  • (M, 0) Outlier detection by expression or splicing (Boyko, Patrick, Olga)
    • Make this an interactive module that updates the metadata as you go along?
  • (H, 0) Splicing modality detection (Olga)
    • Need to add some kind of confidence interval on the modality assignment
  • (M, 0) Splicing
  • (M, 0) Clustergram
    • Highly requested feature. Use seaborn.clusteredheatmap, when it is added.
  • (E, 0) Easy data package creation
    • Using the data packages specification from the Data Protocols people
  • (H, 2) "Monocle" ordering of cells via psuedotime
    • May need to use rpy2? Or rewrite Monocle ourselves using networkx for the minimum spanning trees and such.
    • [Trapnell et al, Nat Biotech (2014)](http://www.nature .com/nbt/journal/v32/n4/full/nbt.2859.html)
  • (H, 1) DownsampledSplicingData
    • Given data created by running MISO or other splicing algorithm, calculate log-log slopes for finding relationships between splicing events detected and sequencing depth.
  • (E, 2) Study/ExpressionData should have option for log base, e.g. if you have raw expresion data and want the log10 transform. But we still need to keep the original data.
  • (E, 2) Refactor Study arguments to expression_kws and splicing_kws because right now there's a whole mess of arguments and it's hard to understand what's required and what's not.
  • (M, 2) Add plots for SpikeInData
    • Violin plots of Spikein concentration vs expression value: Look at what concentration of molecules are detectable
    • Violin plots average distribution of spikein values within a cell
  • (H, 1) Normalize to spikeins
    • Fit a lowess curve to spikein data across concentrations for each cell, then normalize each cell to its spikeins.
    • Also need support for weird configurations, e.g. in the same experiment, celltype A has only spikein X and celltype B has spikeins X and Y, but Y is bigger more reliable set. How do we use the information from celltype B to inform our normalization of celltype A?
  • (H, 2) Identification of cellular subpopulations
    • As described in [Bruggner et al, PNAS (2014)](http://www.pnas .org/content/111/26/E2770.full)
  • (E, 1) Security
    • Write up a document or disclaimer indicating to users that distributing their data this way is not completely secure. This is important for those working with clinical data shoe data storage and analysis tools must pass the United States' [HIPPA](http://en.wikipedia .org/wiki/Health_Insurance_Portability_and_Accountability_Act) regulations.
  • (M, 1) Everything in Fluidigm's [SINGuLAR Analysis Toolset](http://www .fluidigm.com/singular-analysis-toolset.html), including:
    • Outlier analysis
    • ANOVA
    • DataFramePCA
    • Hierarchical Clustering and heatmaps

After this release, we will add:

  • (H, 1) Support for other species. Currently only have hand-curated datasets created for hg19 and mm10.
    • Possibly through hooks into ENSEMBL/NCBI/other biological databases?
  • (H, 1) Examples of real single-cell datasets analyzed through flotilla, and all their figures re-created. Candidate papers:
    • [Trapnell et al, Nat Biotech (2014)](http://www.nature .com/nbt/journal/v32/n4/full/nbt.2859.html)
    • [Shalek et al, Nature (2014)](http://www.nature .com/nature/journal/v510/n7505/full/nature13437.html)
    • [Patel et al, Science (2014)](http://www.sciencemag .org/content/344/6190/1396.abstract)

Note: Abstract for [Biological Data Science](http://meetings.cshl .edu/meetings/2014/data14.shtml) due August 22nd

Fall 2014

At this point, we aim to primarily use and distribute Flotilla on Amazon EC2 clusters.

  • (H, 1) Integration with pybedtools, pysam, and possibly metaseq to quickly grab conservation or genomic region information given gene names.
  • (H, 3) DNA-seq analysis, as in the [SINGuLAR Analysis Toolset](http://www .fluidigm.com/singular-analysis-toolset.html). Input is VCF files.
    • Variant quality and performance
    • Manhattan plots
    • Variant clustering