Proportal ToDoList
To-do List
| id | description | Status | Comments |
|---|---|---|---|
| 1 | Orphan records in DB | To be confirmed: whether remove them or fix the wrong links. | Add your comment |
| 2 | Add/update 13 Cyanophage genome strains into production server | To be confirmed: published or not published data? | Add your comment |
| 3 | Modify the search page | On hold: to be systematically modified for accurate results. | Add your comment |
| 4 | Datasets download | On hold: wait for new datasets released or published. | Add your comment |
| 5 | Datasets upload | Open for suggestion: mechanisms for incorporating the community efforts. | Add your comment |
| 6 | Pipeline for cluster analysis | On going. | Add your comment |
| 7 | Dynamic presentation of cluster network | On going. | Add your comment |
| 8 | Annotation pipeline | On hold. | Add your comment |
Cluster Analysis
Coming soon.
Annotation Pipeline
September 9, 2011
katya: Would you guys be available next week to discuss setting up a pipeline for reannotating some of our newer phages, e.g. the strange new siphos, which were pitifully annotated by the Broad pipeline? (I'd also like to revisit a couple of the myos that were annotated by Matt's group once we have a pipeline we're happy with in place.)
September 21, 2011
Simon: I met Matt Henn last Friday and we talked about the phage annotation pipeline. We can send them our sequences for annotation but both of us would prefer to have the pipeline independent. The problem is (or are) that there are in-house dependencies linked to the annotation pipeline. So to make it public, we would need to remove/move these. Matt estimate that it could be between 3-4 months of work for one person.
Data Download
September 30, 2011
We should add the iron microarray data since it is published. The Supp Info of the paper does not include the entire microarray dataset, only the differentially expressed genes in MED4/MIT9313.
Here's the data as log2 fold change. The 70 (and 72) hour time points come after an iron rescue to the experiment (-Fe) treatment.
September 23, 2011
The data posted for the different papers should look much more professional, or take it down. The names of the files are hokey, and not transparent, for one thing... (that would be easy to fix).
More importantly, the spread sheets for the temp and light data have those messy graphs on them. We should delete the graphs. And there is no annotation on the spread sheets so they would not be useful to anyone, and they don't have units. And they have too many significant figures. Just not ready for the public eye. Just too "raw" to have out there for the whole world to see.
The data we have under the different publications: http://proportal.mit.edu/download/ We probably should take some of it down for now until we can figure out how to clean it up. We should discuss in the next lab meeting.
Data Upload
A number of new strains should be uploaded into the DB. Refer to the Strain Discussion for more detail.
