new results

docs/source/index.rst

@@ -37,6 +37,7 @@ MGEScan on Amazon Cloud (AWS EC2).
    ltr
    nonltr
    visualization
+   results-updated
    results
    source
 

docs/source/results-updated.rst

@@ -0,0 +1,78 @@
+Test Results (New)
+===============================================================================
+
+.. sidebar:: Page Contents
+
+   .. contents::
+         :local:
+
+Three genomes were tested with MGEScan-LTR and MGEScan-nonLTR programs.
+
+* Test genome sequences:
+   - D. melanogaster (dm3): `fruitfly.org <ftp://ftp.fruitfly.org/pub/download/compressed/na_whole-genome_genomic_dmel_RELEASE3.FASTA.gz>`_
+   - C. elegans: `wormbase.org <ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.PRJNA13758.WS251.genomic.fa.gz>`_
+   - A. thaliana: `nih.gov <ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.fna.gz>`_
+* Test Environment: 
+   chameleoncloud.org
+* Hardware Spec: 
+   - Intel Xeon E5-2670 v3 “Haswell” processors (each with 12 cores @ 2.3GHz)
+   - 48 vCPUs
+   - 128 GiB 
+* Operating System:
+   - Ubuntu 14.04 LTS
+
+**Performance nonLTR with MPI**
+
+.. image:: images/results.mpi.nonltr.png
+
+**Performance LTR with MPI**
+
+.. image:: images/results.mpi.ltr.png
+
+`ipynb file <https://github.com/MGEScan/evaluation/blob/master/results/mgescan.ipynb>`_
+
+D. melanogaster (dm3)
+-------------------------------------------------------------------------------
+
+* results (gff3): https://github.com/MGEScan/evaluation/tree/accuracy-evaluation/results/dm3
+
+Evaluation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. list-table:: Elapsed time for MGEScan-nonLTR (dm3)
+   :header-rows: 1
+
+   * - Elapsed Time
+     - Options
+   * - 5 mins (318 secs)
+     - 12 MPI Processes
+   * - 11 mins (610 secs)
+     - 8 MPI Processes
+   * - 12 mins (684 secs)
+     - 4 MPI Processes
+   * - 18 mins (1037 secs)
+     - 2 MPI Processes
+
+.. list-table:: Elapsed time for MGEScan-LTR (dm3)
+   :header-rows: 1
+
+   * - Elapsed Time
+     - Options
+   * - 18 mins (1081 secs)
+     - 6 MPI Processes
+   * - 30 mins (1788 secs)
+     - 4 MPI Processes
+   * - 28 mins (1685 secs)
+     - 2 MPI Processes
+   * - 45 mins (2680 secs)
+     - 1 MPI Process
+
+C. elegans
+-------------------------------------------------------------------------------
+
+* results (gff3): https://github.com/MGEScan/evaluation/tree/accuracy-evaluation/results/c_elegans
+
+A. thaliana
+-------------------------------------------------------------------------------
+
+* results (gff3): https://github.com/MGEScan/evaluation/tree/accuracy-evaluation/results/a_thaliana