At some point in the evolution of every biopharmaceutical company, they’re faced with the problem of finding new targets to keep their pipeline fully loaded. Usually, they’ve exhausted the existing set of targets that they were working on, and are trying to decide what’s next? The answer to that question results from a lot of […]
Public Cloud Databases For Bioinformatics Read More »
I sometimes get asked how I keep up to date with various discoveries and technologies. The simple answer is: RSS feeds. What’s RSS? The short answer is, it’s a means to collect news articles and journal articles without having to visit each individual site. The long answer… is available on wikipedia. I use Google Reader
Mining RSS Feeds For Cancer News Read More »
After my recent post on the current state of pancreatic cancer research, a reader got me wondering if we are indeed making any measureable progress towards understanding and treating pancreatic cancer. My first thought was that a simple year-by-year count of the papers on the subject would give me a crude measure. I’d been itching
Pancreatic Cancer: Are We Making Any Progress? Read More »
At this week’s Bioinformatics Lunch Forum we discussed the first in the upcoming series of Hackathons designed to help bioinformatics and cheminformatics professionals learn about new technologies in an informal and hands-on environment. In general, Hackathons are intended to be free, informal gatherings, with an emphasis on practical, hands-on learning. They can also serve as
San Diego Bioinformatics Lunch Forum: Hackathons Read More »
It’s been a pretty busy weekend, and the recent work on BioGroovy 1.0 is part of the reason. One of the goals of the BioGroovy project has been to leverage the Java libraries that are currently available, and the samples shown on the BioGroovy website reflect its ties to the BioJava library. With this latest
BioGroovy 1.0 Classes Released Read More »
Here’s this weeks crop of papers on the Pancreatic Cancer Genomics Group on Mendeley: The expression and functions of microRNAs in pancreatic adenocarcinoma and hepatocellular carcinoma. Angiotensin II type 2 receptor blockade inhibits fatty acid synthase production through activation of AMP-activated protein kinase in pancreatic cancer cells. Aspirin, nonsteroidal anti-inflammatory drugs (NSAID), acetaminophen, and pancreatic
Pancreatic Cancer Genomics Links Read More »
In previous blog postings, I’ve mentioned the fact that I’m a fan of the Mendeley website. It’s a great tool to let scientists share papers that are considered significant to a particular area of study. In my case, I’m interested in cancer biology, so I started a Pancreatic Cancer Genomics Group in Mendeley. Each week,
Pancreatic Cancer Genomics Group Read More »
The Semantic Web and Drug Discovery was a recent topic at the San Diego Informatics Lunch forum. This is an informal get-together of bioinformatics and cheminformatics practitioners to share ideas and discuss how different technologies can be applied in our disciplines. The topic arose because although the Semantic Web has been talked about for nearly
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Social Media for Scientists was the latest topic at this month’s San Diego Informatics Lunch Forum meeting. Rich Apodaca of Metamolecular discussed his experiences in creating the Chempedia Labs site. This site, based on the Biostar, and Stack Overflow sites, is designed to help chemists ask and answer chemistry related questions and is one of
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The PubMed Central Open Access archive, contains the full text of a subset of the articles available through PubMed. It’s very useful for text mining. In this blog entry, I’ll show you how to search for and download the XML-encoded articles using a simple BioGroovy shell script. To perform the search, we’re going to use
Downloading PubMed Articles Read More »
