Molecular biology archives

The National Library of Medicine, a constituent institute of the National Institutes of Health, announces the release of an extensive selection from the papers of Sol Spiegelman (1914-1983), a pioneering molecular biologist whose discoveries helped reveal the mechanisms of gene action and laid the foundations of recombinant DNA technology, on the Profiles in Science website.

In a separate development, the notebooks used by Fred Sanger, Britain's most decorated scientist, to record experiments that won him two Nobel prizes have been saved for the nation, reports the Observer on 5th August . The Wellcome Trust has stepped in to take possession of the books in which Sanger noted down the progress of research that led to his winning a chemistry Nobel prize in 1958 and a second in 1980, a chemistry double that has never been matched. 'Sanger was the father of genome sequencing,' said Clare Matterson of the Wellcome Trust. 'With his notebooks, we now have a clear record of his influences and thought processes. It would have been tragic if these notebooks had ended up outside Britain.'

PubMed browser compatibility

NCBI has completed work on a new system that forms the foundation for the next generation of new features and capabilities for PubMed and the other NCBI databases. Users may need to upgrade or change to another browser.

PubMed has been tested on the following browsers although other versions may work without difficulties:

Browsers that have been exhaustively tested:

• Windows: IE 7.0, IE 6.0, Firefox 2.0, Opera 9
• Macintosh: Safari 2.0 on OSX 10.4, FireFox 2.0 on OS X 10.2-10.4, Opera 9
• Solaris (Sun OS 10): FireFox 2.0, Opera 9

Browsers that have been tested and seem to work reasonably well:

• Windows: FireFox 1.5, SeaMonkey 1.1.2, Netscape 8.2 & 9.0
• Macintosh: FireFox 1.5, iCab on OS 9 (with some problems)

Browsers that do not work well and should be upgraded:

• Windows: Netscape 7.2, Mozilla 1.7, IE 5.0, IE 5.5 SP2
• Macintosh: Safari, all pre 2.0 versions, Mozilla 1.7, IE (Microsoft no longer supports Macintosh IE, please try another browser such as Safari, FireFox or iCab)

Information taken from:
http://www.ncbi.nlm.nih.gov/entrez/query/static/faq.html#browsers

The Hippocampus book

I can never see the point of book reviews that don't tell you

1. whether the book is worth reading/buying
   
2. anything about what the book contains
   

Luckily the latest oeuvre* from Tim Bliss (late of NIMR's Division of Neurophysiology) has been well-served with two glowing reviews, one today in Science and another in May's Nature Neuroscience.

The review in Science said:

"...with a gestation period of 20 years, written by a team of 23 researchers, styled by 5 editors, weighing nearly 6 pounds, and running over 850 pages [the book] summarizes 50 years of anatomical, physiological, and behavioral research on the sea horse-shaped structure buried deep within the brain's medial temporal lobe. It is, however, much more than a reference work. The book also captures the lore of the field and will serve as a reliable guide for the next generation of hippocampologists."

The reviewer goes on to describe the various chapters, in enthusiastic tones. He ends:

The hippocampus has served as a Rosetta stone, and deciphering its secrets is helping us to understand many core principles of brain function. The Hippocampus Book records the impressive results of our decoding to date and passes the torch to the next generation.

The Nature Neuroscience review was rather more poetic and less enumerative, but leaves us in no doubt about his view of the worth of the book:

"this most magnificent compilation ever written about the the hippocampus in the brain ... serves as a precise guide to hippocampal discoveries, and hence we can forget about PubMed: here we have almost all of the important information about the hippocampus, in context".

Although I can't imagine ever "forgetting about PubMed" I see what he means.

He closes his review thus:

The elusive sea dragon of the brain is guarding its secrets tightly, leaving future researchers plenty to study and discover.

---

* The book in question is:
The Hippocampus Book
Edited by Per Andersen, Richard Morris, David Amaral, Tim Bliss and John O'Keefe
Oxford University Press, 2006
872 pp, hardcover , $125.00
ISBN 0195100271

We do have a copy in the Library if you want to read it for yourself.

NLM advice on web browsers for using PubMed

Which Web browsers will work with PubMed?

PubMed has been tested on the following browsers although other versions may work without difficulties:

Browsers that have been exhaustively tested:

• Windows: IE 7.0, IE 6.0, Firefox 2.0, Opera 9
• Macintosh: Safari 2.0 on OSX 10.4, FireFox 2.0 on OS X 10.2-10.4, Opera 9
• Solaris (Sun OS 10): FireFox 2.0, Opera 9

Browsers that have been tested and seem to work reasonably well:

• Windows: FireFox 1.5, SeaMonkey 1.1.2, Netscape 8.2 & 9.0
• Macintosh: FireFox 1.5, iCab on OS 9 (with some problems)

Browsers that do not work well and should be upgraded:

• Windows: Netscape 7.2, Mozilla 1.7, IE 5.0, IE 5.5 SP2
• Macintosh: Safari, all pre 2.0 versions, Mozilla 1.7, IE (Microsoft no longer supports Macintosh IE, please try another browser such as Safari, FireFox or iCab)

Chemistry Databases fixed

We are currently unable to connect to MDL CrossFire to access the Beilstein and Gmelin databases. The problem has been reported to MIMAS who provide the service and they are investigating.

Update: 5.30pm
Access has been restored. It was due to unannounced changes in our local firewall. Computing have been made aware of the consequences of their actions.

Elsevier electronic books

Elsevier are allowing us to access 500 of their ebooks until 1st September 2007, as a free trial. The books are available on ScienceDirect - you can see a list of the books available (but note that this also includes the Elsevier book series that we already subscribe to).

Some of the books available are

• Antigenic Variation
• Biochemistry and Molecular Biology of Parasites
• Biotechnology and Safety Assessment (Third Edition)
  
• Cell Physiology Source Book (Third Edition)
• Computational Systems Biology
• Dendritic Cells (Second Edition)
  
• Drosophila
  
• Eukaryotic Transcription Factors (Fourth Edition)
• Handbook of Developmental Neurotoxicology
• Heart Development
• Insect Molecular Genetics (Second Edition)
• Molecular Biology of B Cells
• Molecular Endocrinology (Third Edition)
• Mouse Development (First Edition)
• PCR Applications
• Principles of Cloning (First Edition)
• Research Proposals (Third Edition)
• RNA Methodologies (Third Edition)
• Scientific Papers and Presentations (Second Edition)
• Signal Transduction (First Edition)

New websites from Nature

Nature are launching new websites right left and centre at the moment. They have just announced two new services:

Nature Precedings is for the things in life that come before, or support, the published paper. You’re encouraged to upload and view slides, posters, white papers, unpublished manuscripts and other such material. Users can download the documents, vote and comment on them. As the site is brand new, they’re looking for early adopters and to upload files and test out the systems – so have a go. The idea of this new site is discussed in a news item in The Scientist.

Scintilla is a website you can customize to display the latest content from your favorite news sources, science blogs, journals, podcasts and the various other media that make up the increasingly diverse ecology of scientific information. You can rate, recommend and find similar items.

Online tuberculosis textbook

Tuberculosis 2007 is a medical textbook that provides a comprehensive and up-to-date overview of research, diagnosis and treatment of tuberculosis. The 687 page work is available free electronically as a single PDF or a series of PDF files.

The preface says:

Tuberculosis 2007 is the result of a joint effort in response to the Amedeo Challenge to write and publish a medical textbook on tuberculosis. This non-profit-making initiative is particularly attractive due to several reasons. First, the medium chosen for dissemination: the book will be readily available on the internet and access will be free to anyone. Second, its advantage over books published via traditional media is the ease to update the information on a regular basis. Third, with the exception of Spanish and Portuguese, no copyright is allocated and the translation of Tuberculosis 2007 to all other languages is highly encouraged.

http://www.tuberculosistextbook.com/

Patents are useful in biology

A letter in the current Nature highlights the utility of patents as sources of information for biologists.

Thanks to the strict enablement requirements of patent law and patent offices in relation to inventions, one can often find more detailed methodology in patent documents than in journals with severe page limits.

A very good example of comprehensive detail in certain non-embryonic stem-cell methodologies is a PCT application WO/2006/028723 (Non-Embryonic Totipotent Blastomer-Like Stem Cells and Methods Therefor), which includes surgical procedures in organ removal, isolation of cells, and composition and preparation of culture media. In this instance, the level of detail and volume of text relating to methodology far exceeds that which many peer-reviewed journals can accommodate.

Current Protocols in Stem Cell Biology

Latest on the stem cell publishing bandwagon is John Wileys, with another addition to their Current Protocols series.

Current Protocols in Stem Cell Biology will launch online in June 2007, and will be available to Wiley InterScience customers for a free, site-wide trial through December 2007. This title will publish online only, and will be the first Current Protocols title with monthly updates.
Published in affiliation with the International Society for Stem Cell Research (ISSCR), Current Protocols in Stem Cell Biology will cover "the most fundamental protocols and methods in the rapidly growing field of stem cell biology". The title will evolve continuously, adding the latest developments and breakthroughs in the field, and will include "methods and insights that will enhance the progress of global research".

NCBI Newsletter

The latest issue of NCBI News is now available online. Short articles on the following are included:

• PubMed's AbstractPlus display - the new default display
• CD Tree - a program for manipulating and analysing conserved domain records
• Cn3D 4.2 - a new version of the 3D structrue viewer
• Whole Genome Shotgun Growth
• New BLAST View Options
• New Genome Builds—Map Viewer

Encyclopaedia of Life covers all species

Leading scientists and scientific institutions from around the world have announced the launch of the 'Encyclopedia of Life', an international initiative which plans to document all 1.8 million named species of animal, plant and other forms of life on Earth. The initiative brings together species and software experts, who will collate detailed information on all known species, which will be made freely available online to scientists, students and the general public. In addition to written information, photographs, video, sound, maps and other multi-media information is likely to be included in the encyclopaedia.

'The Encyclopedia of Life will provide valuable biodiversity and conservation information to anyone, anywhere, at any time,' said Dr James Edwards, who has been named Executive Director of the project. 'The Encyclopedia of Life will ultimately make high-quality, well-organised information available on an unprecedented level. Even five years ago, we could not create such a resource, but advances in technology for searching, annotating and visualising information now permit us, indeed mandate us, to build the Encyclopedia of Life.'

Blogs and science - 2

Two other blog-related stories also highlight the way that blogs are getting noticed.

1. PhD student Shelley Batts was threatened with legal action for posting figures from the Journal of Science of Food and Agriculture on her blog. The Society of Chemical Industry, owners of the journal, later apologized to her, saying that it was due to an over-enthusiastic staff-member. The Scientist has the full story.

2. Another PhD student, Reed Cartwright, posted some thoughts he had about an alternative explanation of results reported in a genetics paper. It was a little outside his field so he didn't attempt to pursue the idea. Six months later someone else had the same idea and seeing it also on Cartwrights blog he got in touch to invite Cartwright to be a co-author. Again the full story is in The Scientist (this one needs a subscription, or see the print version - Vol 21, Issue 4; page 21). They also mention some other similar tales.

Blogs and science - 1

Blogs are getting noticed more and more in science. Just as I was gearing up to write a little review of science blogs into my inbox pops a lovely article in the latest issue of Cell that has done the job for me. Scientists Enter the Blogosphere by Laura Bonetta (Cell 129(3), 4 May 2007, Pages 443-445) notes that

1,000 or so science blogs provide authoritative opinions about pressing issues
in science, such as evolution or climate change, or aim to engage other
scientists in open and frank discussions about the scientific literature or
science policy.

She gives a number of links, including links to some key finding aids. She also mentions the phenomenon of "Blog Carnivals". Wikipedia explains:

A Blog Carnival is a type of blog event. It is similar to a
magazine, in that it is dedicated to a particular topic, and is published on a
regular schedule, often weekly or monthly. Each edition of a blog carnival is in
the form of a blog article that contains permanent links to other
blog articles on the particular topic. ... Communities of blog readers, writers, and edition hosts form around specific carnivals.

Some that are not mentioned in the article include

• Bio:blogs - a blog carnival covering bioinformatics and computational biology
• Pedro Beltrao's blog on (mainly) bioinformatics
• Seven Stones - EMBO's new systems biology blog

EMBO Systems Biology Blog

The Seven Stones is the blog of Molecular Systems Biology, the open-access journal published by the Nature Publishing Group and EMBO, which covers all aspects of the rapidly growing and interdisciplinary field of systems biology at the molecular level. The topics that will be discussed will include all aspects of Systems and Synthetic Biology, including technical matters, general scientific issues and societal aspects.

Personal laptops

The NIMR Safety Committee have advised that Library users should not be using any electrical equipment in the Library that has not been PAT tested. The Library rules have therefore been amended to include the following rule:

Users should ensure that any personal electrical equipment used in the
Library (e.g. laptop computers) should have an up to date PAT test to ensure
electrical safety.

Users are asked to take note of this safety requirement.

Problems at Nature

Nature Publishing Group are having some technical difficulties and we are experiencing intermittent problems in accessing their online journals. They hope to have the problems resolved very soon.

Wellcome Library reopens

The Wellcome Library is now open with superb new facilities and spaces, having returned to its historic home at 183 Euston Road, London. It is now part of Wellcome Collection, an exciting new cultural destination exploring health and wellbeing through medicine, life and art, which opens in full on 21 June 2007. As well as the Library, the building will house three exhibition galleries, a public events space, a café, a bookshop, a conference centre and a club.

At the opening of the Library last night Mark Walport (Director of the Wellcome Trust) emphasised the importance of the Library to the Trust and outlined the breadth of their collections. The Library was formally declared open by novelist Sebastian Faulks who paid homage to the help he has received from the Library, particularly in researching his 2005 novel Human Traces.

Library closed Saturday afternoon

On Saturday 14th April the Library will be closed between 3pm and 5pm.

SCOPUS downtime 14th April

SCOPUS will be down for maintenance for approximately 4 hours starting at 1pm on Saturday 14th April.