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January 25, 2007
NCBI Courses Offered at the U of I in April
The University of Illinois Biotechnology Information Center, a virtual branch of the U of I Library, and the Roy J. Carver Biotechnology Center are hosting the presentation of two NCBI minicourses and an in-depth course on using the NCBI structure analysis tools. The three courses being offered are:
- Minicourse #6, EntrezGene Quick Start
- Minicourse #11, Microbial Genomes Quick Start
- Exploring 3D Molecular Structures Using NCBI Tools.
The two minicourses will be offered on Wednesday, April 4th; they are each 2.5 hours long. The structure course will be offered on Thursday, April 5th, and is 5 hours long.
To learn more about the courses and to register, please follow this link.
Posted by Katie Newman at 7:09 PM
Publish Videos of Your Experiments Online - for Free
The Journal of Visualized Experiments (2006-) is truly living up to the old adage that a picture is worth a thousand words. This online, open access journal is
publishing visualized (video-based) biological research studies. This publication aims to solve some of the most difficult problems in the contemporary life science research:
- low transparency and reproducibility of biological experiments
- time-consuming learning of experimental techniques
Each video-article will include step-by-step instructions on an experiment, a demonstration of equipment and reagents, and a short discussion by experts describing possible technical problems and modifications. Every scientist planning on a biological experiment will be able to access the database, find videos relevant to their work, and use them as protocols. High effectiveness of visualized instructions, as compared to currently used written protocols, will decrease failure rates for biological experiments, and, thus, facilitate significant savings in time and cost. It will also increase reproducibility of published experiments, one of the main problems in the current life science research.
There is no charge to authors to submit or have their protocols published. Each submission will be reviewed by members of an editorial board, but, at this time, will not be rigorously peer-reviewed (that will come later). The time lapse from the date of submission to the date of publication should be no longer than 7-14 days. At the present time, there are 17 videos available in JoVE.
Of course, researchers have been putting their videos up on their personal websites and in sites such as YouTube. See for yourself: search for microarray in YouTube or in GoogleVideo.
Posted by Katie Newman at 10:14 AM
January 19, 2007
Editor of Open Access Scholarly Journal to Speak
Henry Hagedorn, editor of the open access journal, Journal of Insect Science, will present a talk entitled "Open Access: The revolution in academic publishing".
Where/When:
Monday, January 29th, 4:00 PM, Room B102, Chemical & Life Sciences Building, 601 South Goodwin Avenue, Urbana, IL.
In 2000 Hagedorn resigned as editor of the Archives of Insect Biochemistry & Physiology in order to launch the open access Journal of Insect Science. He recently retired from the University of Arizona, but continues to serve as editor of the Journal which is now supported in part by his new home base at the University of Wisconsin-Madison.
In an open letter published in the Journal of Insect Science, Hagedorn explains his motivation in starting the new journal in an open access mode.
Please note that the University of Illinois's Library Online Research Resources (ORR) lists three instances of the Journal of Insect Science: BioOne, from the Directory of Open Access Journals [DOAJ], and from PubMed Central. You may also access it by going directly to the Journal's home page, http://insectscience.org/.
The University also still has access to the journal from which Hagedorn resigned in protest, Archives of insect biochemistry and physiology, which is published by Wiley. It appears that both journals are publishing about the same number of articles / year.
Several University of Illinois entomology professors are associated with the Journal of Insect Science: May Berenbaum is on the Advisory Board while Hugh Robertson and Gene Robinson are serving on the Editorial Board.
Posted by Katie Newman at 1:08 PM
January 18, 2007
Statistics on the Planting of Genetically Modified Crops
Some interesting year-end statistics from CropBiotech showing the rapid spread of biotech crops across the globe as we progress into the second decade of biotech crops. CropBiotech is produced by the International Service for the Acquisition of Agri-biotech Applications (ISAAA):
In 2006, over 100 million hectares* (250 million acres) were planted in biotech crops. [KN: According to the FAO (2000), there are 1,397 million hectares of arable land, so that means that biotech crops are being planted on about 7% of the arable land.]In 2006, biotech crops were grown by approximately 10.3 million farmers, up from 8.5 million farmers in 21 countries in 2005. Notably, 90%, or 9.3 million of the beneficiary farmers were small resource-poor farmers from developing countries.
In 2006, 22 countries grew biotech crops, 11 developing countries and 11 industrial countries. They were, in order of acerage: USA, Argentina, Brazil, Canada, India, China, Paraguay, South Africa, Uruguay, Philippines, Australia, Romania, Mexico, Spain, Colombia, France, Iran, Honduras, Czech Republic, Portugal, Germany, and Slovakia.
Though the EU countries have traditionally been resistant to planting biotech crops, a quarter of the EU countries are planting biotech including Spain, France, Czech Republic, Portugal, Germany, and Slovakia.
In 2006, biotech soybean continued to be the principal biotech crop in 2005, occupying 58.6 million hectares (57% of global biotech area), followed by maize (25.2 million hectares at 25%), cotton (13.4 million hectares at 13%) and canola (4.8 million hectares at 5% of global biotech crop area).
In 2006, herbicide tolerance in soybean, maize, canola, cotton and alfalfa continued to be the most dominant trait occupying 68% or 69.9 million hectares followed by Bt insect resistance at 19.0 million hectares (19%) and stacked traits, where more than one biotech trait has been breed into a crop, occupied 13.1 million hectares (13%).
Global accumulated impact of biotech crops for the decade 1996 to 2005, in terms of net economic benefits to biotech crop farmers, was $27 billion ($13 billion for developing countries and $14 billion for industrial countries). The accumulated reduction in pesticides from 1996 to 2005 was 224,300 MT of active ingredient, equivalent to a 15% reduction in the associated environmental impact of pesticide use on these crops.
*One hectare equals 2.47 acres.
Posted by Katie Newman at 10:36 AM
January 9, 2007
Open Access: the View from a Scholarly Society's Journal Editor
Starting with the January 2007 issue of the journal Plant Physiology, all articles published by members of the scholarly society that publishes the journal, the American Society of Plant Biologists (ASPB), are open access at no additional cost to the member. Of the 43 articles in the January issue, 25 are freely available to all scholars with no lag period. Some of these may have been authored by non-members who paid $1,000* in order to provide open access to their article, but I suspect not many. [*$1000 if the corresponding author's institution does not subscribe to Plant Physiology, if it does subscribe it is $500.]
The editor of the journal, Donald Ort of the University of Illinois, wrote an editorial for the ASPB News, "Real-Time Plant Physiology: My View of What’s in It for Authors, the Journal, and ASPB". Following several avenues of analysis, he concludes that open access articles are more highly read than non-open access articles, which in turn he feels will enhance the stature of the journal. He also presents an interesting table listing the top 10 plant research journals and their open access option. Most have a provision for open access if the author pays; Plant Physiology will be the only one that offers free open access publishing to it's member authors. Of course, another perk with offering free open access publishing to members might be a jump in the membership count.
Interestingly, the editorial that Ort wrote for the ASPB Newsletter was only available online to members until he deposited it in the University of Illinois' digitial repository, IDEALS, where it is now freely available to all. I would recommend it to the editors of other scholarly journals.
It can also be noted that the ASPB has for several years provided free online access to The Arabidopsis Book through a collaboration with BioOne.
Posted by Katie Newman at 3:56 PM
Using CrossSearch to Search Multiple Databases Simultaneously
You may now search several literature indexes simultaneously using the Web of Knowledge search engine:
While searching multiple databases simultaneously in Web of Knowledge (WoK) is handy, it can be tricky! There are several idiosyncrasies or the WoK search engine that you'll want to be aware of:
1. If you start by searching one database, and then want to do a CrossSearch (cross-db search)...
Say you've done a search in Web of Science (WoS), and then want to search all the other dbs in WoK. You'll see in your Search Results-Summary page a link to: "CrossSearch: View additional results in other databases"
If you click on this link, your search will be run in ALL the OTHER databases, but will only bring back results from the past 5 years!. Note: the results from the db that you started will NOT be in the new search result. If you look carefully at the screen, you'd see what was search, e.g., something like:
topic=(honey bee and varroa) Databases=Biological Abstracts, Food Science and Technology Abstracts, MEDLINE, WCI, Zoological Record, CAB Abstracts, EXCLUDING all records in Web of Science; Timespan=Latest 5 Years
Note carefully the timespan and the exclusion note!
2. If you start your search in the initial CrossSearch screen that is available when you go to the WoK screen (the screen that shows all the dbs in WoK):
your search will by default only come back with results from the past 5 years.
and you can only do a "topic" search (not author)
To get the search to bring back results from ALL years or to be able to specify an author, you need to click on the link to the left of the search input box that says "More search fields". Now you'll see input boxes for topic and author searches, and will have several date range options .
3. When you do a CrossSearch, the results come back in three "folders" labelled:
- ISI WoK Results (includes all the dbs that we pay for, including Medline)
- External Collection Results (includes PubMed, Agricola, and other dbs)
- Current Web Contents
So the results are not all blended together. If you want to look at results from one of the External Collections, you'll be taken out to that search engine; that is, you don't stay in WoK.
4. You can save CrossSearch queries (to be run again) but the system does not let you set up autoalerts with these searches; so autoalerts must be set up for each individual db.
5. You'll need to process your CrossSearch "hits" a little differently than usual when it comes time to print or export the results.
As you're looking at CrossSearch results, you'll frequently see the same citation available through multiple databases. This is so you can see the record in the format used for each db. E.g., you might prefer to see the WoS format, where you can see cited references; or you may prefer to see the CAB format, where you can see the CAB descriptors; etc.
Similarly, if you want to mark any of the records for future printing or export, you'll need to choose which db's record you want to print / export; you do this by "marking" the link attached to whichever db you prefer.
Then, when you get ready to print / export, you'll click on the link to the "marked list". But now, instead of just one marked list, you may have 2-6 marked lists -- one for each database! You'll need to process each list separately, for of course they have different fields in them. While this might not be important for the purposes of printing, it IS important if you're exporting the records into EndNote or RefWorks.
6. The options to refine and analyze by author, institution, subject headings, etc. don't function within CrossSearch search results. . This makes sense, since each of the databases has it's own way of creating the records from which this data would be pulled.
Posted by Katie Newman at 1:41 PM
January 8, 2007
CAB Abstracts, FSTA & Zoological Record
Our means of accessing CAB Abstracts, FSTA & Zoological Record has changed from SilverPlatter (SPIRS) over to the Web of Knowledge search platform. If you have book-marked links to these resources, please change them to the following URLs:
CAB Abstracts: the largest and most comprehensive database devoted to all aspect of agriculture from crop science, animal science, horticulture and forestry to travel & leisure and veterinary medicine.
http://www.library.uiuc.edu/orr/get.php?instid=670820
FSTA: Food Science & Technology Abstracts -- the largest index devoted to food science including food technology, human nutrition, toxicology, packaging and engineering.
http://www.library.uiuc.edu/orr/get.php?instid=670819
Zoological Record: Identifies articles on all aspects of animal biology. Coverage includes behavior, ecology, evolution, morphology, and systematics.
http://www.library.uiuc.edu/orr/get.php?instid=670821
Of course, the URLs are also available in the Online Research Resources directory,
http://www.library.uiuc.edu/orr/
Other databases available in the Web of Knowledge platform are:
The advantages of having these databases in the Web of Knowledge platform include:
- Ability to search all six databases at the same time, should you need to.
- Many links to the full text. Some go directly to the article a "view full text" button; others will be found by clicking on the Discover button
- Direct export of citations into EndNote
- Ability to refine or analyze your results by journal title, author, subject headings, and more
- Many internal linkages
If you need some help making the transition from SilverPlatter to Web of Knowledge search platform, please contact your friendly, helpful librarian!
Posted by Katie Newman at 3:55 PM
January 4, 2007
McGraw-Hill Encyclopedia of Science & Technology -- Online!
We've just gained online access to AccessScience: McGraw-Hill Encyclopedia of Science & Technology Online.
This is the online equivalent of the latest version of the classic McGraw-Hill Encyclopedia of Science & Technology.
AccessScience contains more than 8,500 articles written for students, researchers, and the general public. More than 5,000 scientists have contributed to the Encyclopedia — including 35 Nobel Prize winners. Articles are brought to life by 13,000 high-quality illustrations and rich media content. AccessScience may be searched by keyword or browsed by subject discipline.
Look for these important features in AccessScience...
- full search capabilities of the latest edition of the McGraw-Hill Encyclopedia of Science & Technology
- new trends and developments in science and technology ("Research Updates") from the McGraw-Hill Yearbooks of Science & Technology
- access to 110,000+ definitions from The McGraw-Hill Dictionary of Scientific & Technical Terms
- biographies of scientists
- late-breaking science and technology news
- bibliographies containing more than 28,000 literature citations
- links to evaluated related web sites
- learning resources and study guides
- added illustrations, animations, and image galleries
- questions answered in a weekly Q&A
- and much more
Find the link to this and other electronic journals and reference materials in the Library's Online Research Resource.
Or, you may want to browse Electronic Reference Books for the Life Sciences for other dictionaries and encyclopedias.
Posted by Katie Newman at 5:10 PM
Accessing from Off-Campus: PubMed, Journals and other Library Resources
There are two ways to access Library resources from off-campus. For both of these, you will need to know your UIUC NetID and password. Your NetID is usually the username that precedes your @uiuc.edu email address; your password is usually NOT the same as your email password!
Pros and Cons:
Pro |
Con |
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| Method 1: Use Library-provided URLs to access journals and indexes. |
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| Method 2: Use VPN to provide your off-campus computer with a virtual UIUC IP address. |
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| Recommendation: |
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Method One:
In order to access e-journals and library databases from off-campus, use the links provided from the UIUC Library’s Online Research Resources (ORR) site, http://www.library.uiuc.edu/orr/.
All the resources in the ORR have been registered in a database. When you click on these links from off campus, you’ll be routed through a campus server that will prompt you to provide your NetID and password, thus authenticating yourself as a legitimate UIUC affiliate. Usually you’ll just have to authenticate yourself once per browser session in order to access any library resource.
Example: PubMed
It is particularly important that you use the proper UIUC-specific URL to access PubMed we have created a UIUC-specific PubMed URL that will let you see the e-journals for which UIUC specifically has access. Whether you're on campus or not, this URL will also allow you to see the articles that have been recommended as ‘must reads’ in the Faculty of 1000 database and to see the "Discover" links, which provide you with another avenue for getting to full text and interlibrary loan forms. If you've used the UIUC-PubMed URL from off-campus, you'll be able to click on the links for e-journals that are found within PubMed and gain access to the full text of all the journal articles for which we hold subscriptions.
The standard PubMed URL, which is freely available to the whole wide world, is: http://www.ncbi.nlm.nih.gov/PubMed/
But to be recognized as a UIUC user, and thus to be able to access from within PubMed the UIUC e-journals from off-campus, you should use this URL instead: http://www.library.uiuc.edu/orr/get.php?instid=406312
(You'll find a link for this URL from the Library's ORR page, or from UIUC departmental library homepages such as Biology, Biotechnology Information Center, ACES Funk, and more.)
When you click on the PubMed link from off-campus, you'll be prompted to provide your NetID and password. After you do this, you'll find that you're at the UIUC-specific site for PubMed:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=uiuclib,f1000.
As long as you keep the browser session running, you will remain authenticated as a UIUC affiliate and should be able to click on links for e-journals that are found within PubMed or elsewhere and gain access to the full text of all the journal articles for which we hold subscriptions.
Similarly, if you want to access Biological Abstracts, Web of Science, EmBase, CAB Abstracts, Faculty of 1000, etc., from off-campus: start with the link found in the Library's ORR!
Method Two:
Use CITES' Virtual Private Networking (VPN) to establish a connection to the University, and to authenticate yourself as a UIUC affiliate. When you use VPN to access resources from off-campus, it's as if your computer were physically located on campus! However, in order to use this method, you must be able to install a small program on the computer you are using to access UIUC resources from off-campus. Read more about VPN at http://www.cites.uiuc.edu/vpn/.
Step One:
Download and install the proper VPN program for your computer from CITES.
Step Two:
Download and install the Library profile. (There is just the one library profile file for all computer types.)
Using the VPN program is simple (You'll do this every day):
- Close any browser sessions that may be open on your home computer.
- Start up the VPN program.
- Double-click on Library Profile (you will also see another profile available, "off-campus"; don't use that one!)
- A pop-up screen will appear; login using your NetID and Password.
- Now you may open your browser (Firefox, Netscape, Internet Explorer, etc.)
After you've logged in via VPN, you should be able to go about your business as if you were located on campus as your computer will perform as if it were coming accessing the internet from the UIUC IP range. That is, you can go directly to the publisher's web sites, etc.
Caveat: there are a FEW resources for which the VPN mode of access won't work, usually due to restrictions placed by publishers. In MOST of those cases, you'll be able to get in via the link in the Online Research Resources directory.
Posted by Katie Newman at 3:29 PM