User Performs Action
This is mapped to the beginning of the workflow(A,B) because at the beginning of the experiment the crystallographer must choose which crystal they will use, mount it on the synchrotron and get some diffraction images.
output: jpg and text file??
User Decision Point 1
The first user decision point is mapped to inspect images(E) as after inspecting the images the crystallographer must make a decision as to whether the images are good enough and if the crystal is still ok to use and if not
repeat the first part of the experiment again.
output: a text file containing a yes/no decision??
Exchange Between Services
The exchange between services happens between mosflm and the detector.(C,D,E)
output: a jpg and text file ??
Collection manipulation
This is collection manipulation as the MTZ files are collections of data about spots which start off as unmerged(I) which contains data about the same spot multiple times. It then needs to be rearranged and merged to create a new file(J) which only contains one occurrence of each spot.
output: a list of urls pointing to a series of jpgs and text files??
Running Service with others data
This is mapped to this area of the workflow(L) because when the reflection data is processed to get coordinates, it is compared to the structure of similar proteins from the PDB. This is retrieved from the PBD using a search tool which matches the sequence data of proteins(K). This is then processed using services provided from CCP4.
output: a text file??
Workflow
The workflow is mapped to this section as this part is a linear workflow(M,N,P) which will be automated for our process there are not any particular areas of interest within this from a provenance point of view.
output: a text file???
User Decision Point 2
This is 'check satisfaction of coordinates'(Q) as within this step the user must decide if the coordinates(P) generated through coot are accurate enough and if they are not go back and change them.
output: a text file with coordinates and a text file with a decision??
Publish Data To URL
The data is submitted to the PDB which will then mean it will have a web reference.(U)
output: a url??
Collaborative Editing
This is mapped to the section involving the wiki(W,X,Y), as the wiki is used for discussion and editing of the report by multiple collaborator.
output: a url to a wiki page??
Citing Paper
The data which is in the PDB is now cited in the report(Z) produced by collaboration on the wiki.
output: a pdf with a link to the wiki page??
Credentials
Submitting to the biology journal(AA,AB) fits the credentials section, as to submit to the biochemistry journal, you need to be logged in the the appropriate sort of account.
output: an email with a submission confirmation???
Discovery By Query
Anyone is able to search the Biochemistry journal(AC) through the search link on the main page so the user can query for information about the protein solved in the scenario and discover the report(AD)
output: an html page with a set of query results??
Social Collaboration
Social collaboration in the crystallography workflow is done through use of twitter(AE) to make comments and suggestions about the paper
output: a set of tweets dumped as a text file
--
PaulGroth - 13 Jul 2010
to top