Tag Archives: NCI

Tip of the Week: CellMiner from NCI

CellMiner_tip_imageOnce a month I get a great email from my BioMed Central with suggestions of articles that I might want to read. In a recent edition there were lots of papers I wanted to read.  One of them was “CellMiner: a relational database and query tool for the NCI-60 cancer cell lines” by Uma T Shankavaram et. al. & is the reason for this tip of the week. The paper is very well written, clear, and points out some Excel download pitfalls I’ve struggled with in the past. I figured if their writing is so good, I’d better check out their web resource, CellMiner.

CellMiner is brought to you by the Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), Center for Cancer Research (CCR), National Cancer Institute (NCI) and is created as a “database and query tool designed for the cancer research community to facilitate integration of the molecular datasets generated by the GBG and its collaborators on the NCI-60″. So, without further ado, please watch this tip, read the paper, and then utilize this great resource for your own scientific gains.

ResearchBlogging.org Uma T Shankavaram, Sudhir Varma, David Kane, Margot Sunshine, Krishna K Chary, William C Reinhold, Yves Pommier, & John N Weinstein (2009). CellMiner: a relational database and query tool for the NCI-60 cancer cell lines BMC Genomics, 10 (277) DOI: doi:10.1186/1471-2164-10-277

MatchMiner is -down- UP

Bumped, with update below [Mary]

I went looking to use MatchMiner a couple of weeks ago and couldn’t access the page. But that happens–I worked around that with some different IDs. But yesterday I got an email about the entire server that MatchMiner is on:

Extended, Unplanned Outage on discover.nci.nih.gov
Folks,

Our discover.nci.nih.gov server, the host of GoMiner, MatchMiner and our other applications, is currently offline because of unscheduled maintenance. We expect to have the server back up later in the week. We will post a note back to this list when it is available again.

If you are receiving this message, it is because you have subscribed to the GBG-Announcement list.

Just FYI. I saw some people searching for this since it was down and figured I would mention it as a public service.

If you are curious now about what MatchMiner does, check out Jennifer’s tip on it: Translating Gene IDs with MatchMiner.

UPDATE: MatchMiner is back up:

Folks,

Our server, discover.nci.nih.gov, is now back online. We apologize for any inconvenience this outage may have caused. If still have any problems with access the machine or our tools, please contact us at webadmin@discover.nci.nih.gov.

 

Tip of the Week: Translating Gene IDs with MatchMiner


As we were creating a tutorial on the GoMiner resource from the Genomics and Bioinformatics group at the National Cancer Institute (NCI), we found another handy NCI tool named the MatchMiner.

MatchMiner translates one type of gene ID into another type – essentially the genetic equivalent of Swahili-to-German translating software. In this tip I’ll show you how to do a translation on a list of genes, or a ‘Batch Lookup’.