Babmi? From: Nomi Harris <[email protected]<mailto:[email protected]>> Date: Saturday, February 1, 2014 1:24 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Cc: Nomi Harris <[email protected]<mailto:[email protected]>> Subject: Re: [Release-team] Services to add to or remove from Services page (http://kbase.us/developer-zone/services/) Forgot one: MEME The MEME service integrates the MEME suite of motif-based sequence analysis tools, which enable discovery of novel motifs in collections of unaligned DNA sequences, comparison of discovered motifs, and search for motif occurrences in sequence datasets. On Fri, Jan 31, 2014 at 9:51 PM, Nomi Harris <[email protected]<mailto:[email protected]>> wrote: This is my understanding of which new services need to be added to the Services web page and which are being removed (commented out, mostly, so we can restore them quickly if they are revived). New (user-facing) services in this release [note that I edited some of the descriptions that were in the Master tab because some of them were too wordy] cMonkey: The cMonkey biclustering tool takes as input gene expression data, promoter sequences, and gene-gene functional association/physical interaction data, and finds biclusters of conditionally co-regulated genes. Compression-based Distance (CBD): Compression-based distance (CBD) is a method to efficiently characterize the similarities between microbial communities via the amount of repetition or overlap in order to determine microbial community distance. Expression: This service has methods to retrieve data and metadata for expression samples, as well as methods for data comparisons. Supports microarray, RNA_seq, proteomics, and qPCR. Gene conservation: This module provides services for the evaluation of reliability of cross-species biological network projection to assess gene conservation. Inferelator: The Inferelator algorithm infers regulatory networks from gene expression data. It takes as input cMonkey biclusters, a list of regulators, and (optionally) environment meta-information that describes how the experiments were performed. Interlog projection: This service has methods to project an interlog network of species A from the query network of species B based on ortholog information. The ortholog information is precomputed by the Inparanoid algorithm. M5NR: The M5NR integrates many sequence databases into one single, searchable database. A similarity search (using BLAST or BLAT) allows the user to retrieve similarities to several databases. The M5NR API facilitates mappings between M5NR IDs (sequence md5 checksums) and annotations from databases integrated into the M5NR. Probabilistic annotation: This service computes likelihoods for annotations and reactions for a given genome. Likelihoods are computed based on similarity to genes with literature evidence and genes in subsystems. Commenting out from Services page because service is not currently working: PROM (already commented out) Regulation (regprecise) QC service Fizzy feature selection (removed at Tom Brettin's request on 12/9) I also propose to remove or comment out these two--let me know if I should keep them: Protein info service Translation service (The MO translation component of the translation service translates KBase IDs to MicrobesOnline IDs and vice-versa. These methods are used to retrieve MicrobesOnline annotations (such as orthologs, domains, and operons) for corresponding KBase objects.)