Public Datasets

h1. Public Datasets

NRAMM releases a number of annotated and partially annotated datasets for public use.  For example, some of the datasets are used to test new algorithms for particle picking or CTF correction.  The datasets released so far are listed below with links to associated data and annotations.  Please feel free to let us know at nramm@nysbc.org if you have suggestions for making these datasets more accessible or ideas for other data that might be useful.

The amount of metadata available for each data set varies.  The KLH dataset is old and  included here as it has been used as a standard for a large number  of particle picking papers (see "Zhu _et al._ 2004":http://www.ncbi.nlm.nih.gov/pubmed/15065668).  The GroEL dataset has been used as a testbed at NRAMM for a number of studies ("Stagg _et al._ 2006":http://www.ncbi.nlm.nih.gov/pubmed/16762565 and "Stagg _et al._ 2008":http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2505049).  The 50S ribosome subunit datasets were used to illustrate methods for ab initio reconstruction algorithms ("Voss _et al._ 2010":http://www.ncbi.nlm.nih.gov/pubmed/20018246).  In each case below we provide links to further pages describing the datasets in more detail.  Links on these pages will provide access to the native data (the images) and the means to download it, some of the metadata (e.g. the particle coordinates, defocus values etc.) and when possible links to the images via the Leginon database ("Suloway et al., 2005":http://www.ncbi.nlm.nih.gov/pubmed/15890530) and the processed images via the Appion database ("Lander et al., 2009":http://www.ncbi.nlm.nih.gov/pubmed/19263523).  Within Leginon and Appion the data can be explored in a number of ways and various further metadata is available to explore or for download from these pages.  The best way to figure out what the Appion pages can provide is to just go ahead and explore them by following the links.

h2. Public data sets:

bq. *Note:* Not all sets are currently available. Older sets are in the process of being retrieved from archives and will be available soon.

bq. see also [[Anonymous datasets]]

* *[[Synthetic 70S Ribosome Datasets]]* — synthetic datasets used to evaluate likelihood-based classification in Frealign from "Lyumkis _et al._ 2013":http://www.ncbi.nlm.nih.gov/pubmed/23872434

* *[[KLH datasets]]* — including standard particle "bake-off" dataset from "Zhu _et al._ 2004":http://www.ncbi.nlm.nih.gov/pubmed/15065668

* *[[GroEL datasets]]* — including datasets used for "Stagg _et al._ 2006":http://www.ncbi.nlm.nih.gov/pubmed/16762565 and "Stagg _et al._ 2008":http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2505049

* *[[Ab initio model datasets]]* — the 50S ribosomal subunit from "Voss _et al._ 2010":http://www.ncbi.nlm.nih.gov/pubmed/20018246

* *[[P22 datasets]]* — mature wild type bacteriophage from "Lander _et al._ 2006":http://www.ncbi.nlm.nih.gov/pubmed/16709746

* *[[Lambda virion datasets]]* — mature wild type bacteriophage lambda virions from "Lander _et al._ 2008":http://www.ncbi.nlm.nih.gov/pubmed/18786402

* *[[TMV datasets]]* — unpublished Tobacco Mosaic Virus dataset

h2. Download tool:

 * *[[Dbemwiz|dbemwiz.jar]]* a java based wizard which manages downloading an entire dataset.  This is useful as the datasets can be very large.

h2.  Viewing data and metadata: 

 * See [[appion:Common_Features|Image_Viewers]] for help and instructions on using Leginon/Appion web-based image viewing pages.  Note that you will need to login once as an Anonymous user before you can access the datasets. Summary information may be viewed by selecting the Summary option at the top of the viewer window which will pop up a new window. [[appion:|Appion processing pipeline information]] and all metadata may be accessed by selecting the Processing button at the top of the viewer window which will pop up a new window.