SeekServer

SeekServer runs the coexpression mining algorithm using a multithreaded TCP/IP interface. When it is running, SeekServer services requests from multiple clients over the network. The requests that can be handled by SeekServer are, for example:

• retrieve a list of genes that are found to be coexpressed with the query genes
• retrieve a list of datasets where this coexpression with the query is found to be occurring.

Usage

Basic Usage

 SeekServer -t <port> -x <dset_platform_map> -i <gene_map> -d <db_dir> -p <prep_dir> -P <platform_dir>
 -Q <quant> -n <num_db> -u <sinfo_dir>

This starts an instance of SeekServer on the indicated port and begins accepting client requests.

Client Request Format

When a client request comes in, SeekServer looks for the following sequence of 4 strings in the request message:

• strSearchDataset. Dataset names, as referred by the dset_platform_map, to be used for the search. Delimited by " ".

• strQuery. Query gene names, as referred by the gene_map, separated by " ".

• strOutputDir. Output directory where intermediate results are generated. Must be a directory that the running user of SeekServer has access to. /tmp is recommended.

• strSearchParameter. A string of the form "1_2_3_4" where each number denotes the following:
  1 - the search method, one of RBP, OrderStatistics, EqualWeighting. Recommended RBP (also known as the CV weighting).
  2 - rbp parameter p (a float 0.90 - 0.99). Recommended 0.99.
  3 - minimum fraction of query required to score each dataset (0 - 1.0). Recommended 0 (no minimum).
  4 - distance measure, one of Correlation, Zscore, ZscoreHubbinessCorrected. Recommended ZscoreHubbinessCorrected.
  

See Sleipnir::CSeekNetwork for the specification of an incoming string message.

Once SeekServer correctly receives the above 4 strings, a search instance using the provided search parameters will be initiated on the server side.

Outgoing Message Format

Each outgoing message is generated upon finishing searching the client's query. In general, if the search is successful, SeekServer will send to the clients these two arrays in sequence:

• a binary float array of dataset weights, indicating how datasets are related to the query.
• a binary float array of gene scores, indicating how genes are coexpressed with the query.

See Sleipnir::CSeekNetwork for the specification of an outgoing float array.

Query-independent search setting files and directories

These include the following: dset_platform_map, gene_map, db_dir, prep_dir, platform_dir, quant, sinfo_dir. For a discussion of these files and directories, please refer to the SeekMiner page in section: Query-independent search setting files and directories.

Detailed Usage

package "SeekServer"
version "1.0"
purpose "Performs cross-platform microarray query-guided search in server mode"

section "Main"
option  "port"              t   "Port"
                                string default="9000"   yes
option  "dset"              x   "Input a set of datasets"
                                string typestr="filename"   yes
option  "input"             i   "Input gene mapping"
                                string  typestr="filename"  yes
option  "dir_in"            d   "Database directory"
                                string  typestr="directory" yes
option  "dir_prep_in"       p   "Prep directory (containing .gavg, .gpres files)"
                                string  typestr="directory" yes
option  "dir_platform"      P   "Platform directory (containing .gplatavg, .gplatstdev, .gplatorder files)"
                                string  typestr="directory" yes
option  "dir_sinfo"         u   "Sinfo Directory (containing .sinfo files)"
                                string  typestr="directory" default="NA"    yes
option  "dir_gvar"          U   "Gene variance directory (containing .gexpvar files)"
                                string  typestr="directory" default="NA"
option  "quant"             Q   "quant file (assuming all datasets use the same quantization)"
                                string  typestr="filename"  yes                             
option  "num_db"            n   "Number of databaselets in database"
                                int default="1000"  yes
option  "num_threads"       T   "Number of threads"
                                int default="8"

section "Optional - Parameter tweaking"
option  "score_cutoff"      c   "Cutoff on the gene-gene score before adding, default: no cutoff"
                                float default="-9999"
option  "square_z"          e   "If using z-score, square-transform z-scores. Usually used in conjunction with --score-cutoff"                          
                                flag    off

section "MISC"                              
option  "is_nibble"         N   "If true, the input DB is nibble type"
                                flag    off
option  "buffer"            b   "Number of Databaselets to store in memory"
                                int default="20"
option  "output_text"       O   "Output results (gene list and dataset weights) as text"
                                flag    off
option  "additional_db"     B   "Utilize a second CDatabase collection. Path to the second CDatabase's setting file."
                                string default="NA"