James Fraser & Michael Eisen: Baseball Meets Biology
Quick post here. I am looking for OpenAccess figures on introductory topics in molecular and cellular biology like DNA, RNA, proteins, transcription, translation, etc. I want these for multiple purposes including teaching, blog posts, etc. Anyone out there know of a database of such things?
Some suggestions from Twitter
- NCBI bookshelf (from jewmanchue)
A bit of a rambling post here but here goes anyway …
Well, normally I have avoided digging in to UC Davis too much here on my blog. Mostly because it does not really fit with the themes of evolution, open access, microbiology, genomics, etc. Plus, overall, I really really like Davis and UC Davis. The town is very pleasant – simple – but very nice. I lived on my bike in the Washington DC area, taking my life into my own hands, and now living in bike town USA is great. In fact, I even have a blog about life in Davis. And UC Davis is overall a great place to be for me, especially with its strengths in evolution and ecology, population biology, and various aspects of microbiology.
But alas, now all is perfect here in blissville. And one thing that drives me crazy is the mind numbing complexity of the bureaucracy. I note, I moved to Davis from The Institute for Genomic Research (TIGR), a small non profit research institute that helped lead the genomics revolution. And mostly I have suffered annoyances of the crazy giant complex system here in silence (except for with a few colleagues here and there). However, I have been planning to start to discuss some of these issues in public more. And just as I was thinking about this, it seems that others are also discussing some issues with the need to reform some UC Davis admin activities.
You see, last year we got a new Chancellor (the name they use here for the head of the University). The new Chancellor is Linda Katehi. I have met her a few times and overall I am very impressed. Perhaps the thing that impresses me most is that in times of somewhat bad financial struggles she has decided to take on the bloat in the administrative side of things as one of her first activities. And it seems this is not all talk. For example our great local newspaper, the Davis Enterprise has been running a series of articles, most by Cory Golden, on some reports and announcements from UC Davis suggesting that Katehi really will be trying to change things around here. Alas, the Davis Enterprise is not available for free on the web for all to read. If you want to get some really insightful stories about UC and UC Davis, you should subscribe. It is not much and if you have any connection to Davis it is worth the money.
Fortunately for me, and perhaps for you, the Davis Enterprise has agreed to let me post extensive quotes from their articles especially as they relate to UC Davis. I will delay a bit in posting to try and respect their need for subscribers (unlike with scientific publications, which should all be open and freely available, I do not feel that way about private enterprises like newspapers). Anyway – I am posting below two stories by Cory Golden of relevance to the UC Davis attempts to change the way things are done here. One is about reorganization of some administrative functions. And one is about an outside evaluating group that just wrote a report on some of the challenges for research at UC Davis. A third is about a campus “vision” statement put out by Katehi.
The main gist is, that UC Davis has enormous potential that is being impeded by some bureaucratic complexities and inefficiencies. Some good quotes include:
Those included “overstaffing, ineffective personnel and playing ‘lawyer games’ to be sure that no risks threaten the organization.”
“Over many decades Davis has developed a culture that permeates its institutions and people, one that can best be described as risk-averse, modest and insular.”
And Katehi seems like she is going to try and fix many of them. No – the plans are not exactly what I would do. But more on that later. The direction things are moving is very appealing to me. I was not inspired by the previous leadership of UC Davis. I am much more hopeful now and am awaiting these changes very impatiently.
Reorganization ramps up at UCD
By Cory Golden
August 18th, 2010
UC Davis leaders have OK’d in spirit a plan to cut up to $16 million in staff positions while rolling campus information technology, human resources and finance offices into a single shared services center.
An all-staff forum about the reorganization is set for Thursday at 10:30 a.m. in the UCD Conference Center Ballroom.
Chancellor Linda Katehi said last week that her goals for the effort, dubbed the “Organizational Excellence Initiative,” are to redirect money to academics, student services and other priorities while improving the service given to the campus.
For now, staff members are left with questions and union leaders have growing concerns.
Among them: how many jobs will be eliminated, how positions in the proposed new center willbe filled, how fast UCD will make the changes and how much money the campus will invest in technology intended to increase efficiency.
Some answers may come from a meeting of the chancellor’s cabinet Aug. 31.
At its last two-hour meeting, last week, the cabinet decided to move forward on the outlines of recommendations made by the Atlanta-based consulting firm ScottMadden, based on more than three months of on-site assessment.
About 6,500 finance, HR and IT employees would be affected by the first phase of the project, as drawn up by the consultant.
“On the amount of savings projected, what percentage of that is from staff positions?” asked a woman in the audience during a presentation Monday to employees of administrative units that would be part of the proposed center.
Answered Karen Hull, associate vice chancellor for human resources, “Those savings reflect staff positions.”
Just how many would be cut, she said she didn’t know.
“We don’t know that for a couple of reasons,” Hull said. “One is that we don’t know for sure whether the cabinet will support the recommendation that ScottMadden has made, so that’s one big variable.
“(It) would be very misleading to connect the (estimated savings) to actual positions,” she added. “There’s a lot of dynamic changes that occur. We have natural attrition every year. We have natural turnover. We have retirements. We will not be wanting to fill any of those positions while we are forming the shared service center.
“I know that it sounds alarming — and it is alarming. These are your jobs, but I think that when we get the picture painted in a more detailed manner it will be more clear as to what will be the potential job loss.”
The consultant found that, at a core cost of $54 million a year, the campus’ human resources, information technology and finance staffing exceeded those of similarly sized organizations.
Among its recommendations: creating a shared structure with one director, improving the use of technology for timekeeping, purchasing, accounting and other tasks, and simplifying policies and processes.
The report pegged one-time or recurring costs, much of it from computer software systems, at about $19.5 million. If UCD follows its suggested timeline, the report says the university should begin saving money in less than three years.
Under the proposed model, about 80 percent of faculty, staff and student questions would be handled through self-service, either through a web portal or interactive phone system.
In what’s likely to be a controversial recommendation, the consultant suggests that the campus create job descriptions for the shared services center, then have employees apply for those positions.
“They recommend kind of an open slate. Everyone has an opportunity, and you compete for those jobs,” Hull explained, adding that the administration may yet choose another way to staff the center.
Among existing problems the consultant’s report pinpointed: large amounts of the same or similar work being done by multiple departments, excessive reviews, delayed service and multiple IT help desks. It also found “manual data collection, transcription of data, high error rates and significant rework.”
One employee at UCD might process about 1,065 invoices per year, working on paper with a long approval process. At Johns Hopkins University, which uses a shared service center model and automated system, one employee can process 45,000, the report says.
Union leaders interviewed Tuesday wondered aloud if the reorganization was an attempt to weed out their members.
Dorie Decosta, president of UCD’s chapter of the Coalition of University Employees Local No. 7, said there was a “general feeling of unrest and discomfort” among staff.
The prospect of automation replacing personalized customer service “sounds like hogwash,” she said.
“You need that element of continuity and what UCD says it stands for: caring about students, caring about staff, caring about faculty.”
Wrote Susan McCormick, president of the University Professional and Technical Employees Local No. 6, in an e-mail message, “I am getting the feeling that UC is finding ways to eliminate the highest-paid employees. They are eliminating at the top of the pay scales, those at UC the longest and those with the most knowledge.”
ScottMadden’s contract calls for a fee of $350,000, plus up to $70,000 in expenses.
The proposed reorganization comes as UCD continues to grapple with an unprecedented $150 million in state budget cuts since 2008-09. It has cut 1,062 positions: 459 layoffs or employees who had hours cut, the rest through attrition or voluntary separation.
The campus has cut 30 percent of its administration’s core budget, compared to a 15.4 percent cut for academic units.
UCD faces another $38 million to $78 million shortfall depending on the outcome of state budget talks this year.
Reports rap UCD research
By Cory Golden
August 15th, 2010
Katehi details campus vision
By Cory Golden
July 30th, 2010
I am teaching a class this spring and as part of the class am having one lecture on “Phylogenetic trees and methods.” I would like to link to (and be able to mix and match material from) some review paper on this topic. So I am searching for something that is Open Access and preferably with a broad Creative Commons license. Anyone know of anything good?
I just love the continued coverage of the story of the students from Trinity School in New York (a high school) who do investigative DNA barcoding projects. (There is a good new story about this on the LA Times blogs at:Think that sheep’s mik cheese comes from a sheep? DNA doesn’t lie | Booster Shots | Los Angeles Times)
In the most recent example, two students, Brenda Tan and Matt Cost, did some home barcoding in collaboration with people from the AMNH and Rockefeller University.
Among their findings:
- “an invasive species of insect in a box of grapefruit from Texas”
- “what could be a new species or subspecies of New York cockroach”
- multiple mislabelled food products including (quoted from the press release, I note)
- An expensive specialty “sheep’s milk” cheese made in fact from cow’s milk;
- “Venison” dog treats made of beef;
- “Sturgeon caviar” that was really Mississippi paddlefish;
- A delicacy called “dried shark,” which proved to be freshwater Nile perch from Africa;
- A label of “frozen yellow catfish” on walking catfish, an invasive species;
- “Dried olidus” (smelt) that proved to be Japanese anchovy, an unrelated fish;
- “Caribbean red snapper” that turned out to be Malabar blood snapper, a fish from Southeast Asia.
The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “adopt” bacterial genomes, such as those sequenced as part of the “Genomic Encyclopedia of Bacteria and Archaea” (GEBA project), for analysis. This “Adopt a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.
For more information, and to apply for the November 2, 2009 deadline, see:
A much much much older talk, from when we just started the project is here:
Secretary Chu Announces up to $12.5 Million in Recovery Act Funding for New Graduate Fellowships in Science, Mathematics and Engineering
New Funding Highlights the Administration’s Commitment to Empowering Students to Choose Careers in Science
Washington, DC – U.S. Energy Secretary Steven Chu announced today that up to $12.5 million in funding from the American Recovery and Reinvestment Act will be awarded in early 2010 to support at least 80 graduate fellowships to U.S. students pursuing advanced degrees in science, mathematics, and engineering through the newly created Department of Energy Office of Science Graduate Fellowship program. The goal of the fellowship program is to encourage outstanding students to pursue graduate degrees in physics, chemistry, biology, mathematics, engineering, and environmental and computer sciences – fields that will prepare students for careers that can make significant contributions in discovery driven science and science for national needs in energy and the environment.
“Training the next generation of U.S. scientists and engineers is critical to our future energy security and economic competitiveness,” said Secretary Chu. “This Fellowship is part of the Administration’s effort to encourage students to direct their talents towards careers in science and our nation’s next technology revolution.”
To be eligible for the Fellowship, applicants must be U.S. citizens and currently a first or second year graduate student enrolled at a U.S. academic institution, or an undergraduate senior who will be enrolled as a first year graduate student by the fall of 2010. Applicants must be pursuing graduate study and research in the physical, biological, engineering and computational sciences. Interested students can apply online at: http://www.scied.science.doe.gov/SCGF.html
Each fellowship award will be $50,500 per year for three years to provide support for tuition, living expenses, research materials and travel to research conferences. Fellowships will be awarded on the basis of peer review. Applicants may begin submitting applications on September 30, 2009. Completed applications are due November 30, 2009.
I am looking around to find examples of undergraduate programs/majors in genomics or genome biology. I got a couple of potential examples from a post I made on friendfeed but am looking for more. What I am looking for is not just courses in genomics but majors/programs in genomics … do they exist and if so, where and what do they look like. Any information would be helpful. Here is what I have found so far:
- MSU RO: Academic Programs: Genomics and Molecular Genetics
- PLoS Biology – The Undergraduate Genomics Research Initiative
- Meeting Report: Incorporating Genomics Research into Undergraduate …
- MCB Undergraduate Program – Genetics, Genomics & Development
- Genomics/Bioinformatics :: New Option/Minor Proposal :: Curriculum …
- Incorporating Genomics into Undergraduate Curricula at Wheaton College
- Phage Genomics Research Initiative – Division of Biological …
- 123 Genomics – Bioinformatics and Genomics Courses
I just got in the mail some of the free science education DVDs I ordered from the Howard Hughes Medical Institute. The first one I have looked at is quite good (it is on evolution, of course). I recommend people browse the HHMI catalog here. These could be useful for students as well as for actual courses.
And of course, the best part, they are free.