The Merck Index 14th Edition

Latest version of the essential reference book includes searchable CD, and a new upgrade offers extensive structure search capabilities

With more than one million copies sold, The Merck Index has been the primary reference source for generations of professionals looking for precise, comprehensive information on chemicals, drugs and biologicals. The latest 14th Edition of this essential reference work for chemists, biochemists, pharmacists and related professionals, includes with the book, for the first time, a text-searchable CD-ROM, which contains all the data in the book and more. The CD contains ChemFinder, the industry-leading scientific search engine from CambridgeSoft Corporation (Cambridge, Massachusetts) that allows data to be searched by keywords, references and numerical properties.

The Merck Index is a one-volume encyclopaedia of chemicals, drugs and biologicals that contains more than 10,000 monographs, 32 supplemental tables, 450 Organic Name Reactions and more. This 14th Edition has been extensively revised to ensure its accuracy and enhance its readability with many new features as well as thousands of new references, trademarks and uses, plus an expanded – and timely – focus on “Green Chemistry” and compounds of environmental significance. In addition to revisions and updating, enhancements include embedding the Chemical Abstracts Registry Numbers for title and derivative compounds within the monographs.

CambridgeSoft, provider of previous electronic editions of The Merck Index, has made available The Merck Index 14th Edition/Chemists, an upgrade that provides the unique, powerful capability to search the CD to find molecules by fragment, sub-structures or full structures, on the basis of either exact matching or similarity. Structure searching is precise and convenient and includes tautomeric full and sub-structure searching. You can search for structures containing isotopic labels, or tetrahedral stereocenters, or other characteristics.

The Merck Index 14th Edition/Chemists, which is supplied by Adept Scientific (Letchworth, Herts.), provides the ability to search for alternative groups, either in atom labels such as “(OH,H,CONH2,Me)” or drawn using the R-Group features of ChemDraw (CambridgeSoft’s renowned structure drawing software, also available from Adept Scientific). Link nodes are supported, so you can search for variable-length rings and chains such as “(-CH2)6-8-” or multi-connected variables (“-R-“). You can now search for any type of single atom (“A, Q, X, M”) or any group (“R”).

Also included is an Personal Internet Edition subscription that provides immediate access to the data on the CD as well as updates. Together, the CD and the Internet Edition contain all the contents of the printed 14th edition plus nearly 1,000 monographs archived from previous editions.

All CambridgeSoft products, including the latest versions of ChemDraw, ChemOffice, Chem3D, BioDraw, BioOffice, BioAssay and E-Notebook as well as The Merck Index, are available from Adept Scientific.

With offices in the UK, USA, Germany and throughout the Nordic region, Adept Scientific is one of the world’s leading suppliers of software and hardware products for research, scientific, engineering and technical applications on desktop computers.

BioAssay HTS Manages Screening Data for the Harvard Medical School

by Fred Harbinski

Fred Harbinski has a BS degree in Plant Biology from the University of California, Berkeley, where he studied fungal systematics. He followed with two years of graduate work at Harvard University studying deep sea marine biology and bacterial evolution. He currently manages a high throughput facility in the Tosteson Laboratory at Harvard Medical School, where they are screening for inhibitors of translation initiation for cancer therapy.

“WHEN I JOINED the Tosteson Laboratory at Harvard Medical School two years ago, our cancer biology group consisted of just seven individuals: two instructors, two students, two technicians, and one very driven PI. With two functional multi-pipettors between us, pushing fifty compounds a week through our series of biological assays was considered an accomplishment. A series of three-ring binders contained the sum of our labours: carried to every lab meeting, the relative merits of various scaffolds was debated blot by blot, page by page.”

“A tripling in our laboratory size, coupled with the addition of a fully automated high-throughput screening facility, necessitated a revision of our information management system. After a careful review of the available options, we followed the advice of one of our NCI collaborators and became involved in the beta testing of CambridgeSoft’s BioAssay HTS application.”

“The backbone of BioAssay HTS is its virtual plate library, containing information on nearly every 96 and 384 well plate that passes through our screening facility. We began by populating our master plate library with the contents of the NCI Open Chemical Repository, a 3400-plate library containing more than 140,000 compounds. Organised by barcode designation, plates can be viewed in “browse” or “edit” mode, plate or chart form, complete with compound structure. A search function makes locating individual compounds relatively easy. A click on any given well brings up a subwindow displaying relevant compound attributes such as molecular weight, formula, and solubility, as well as quantity remaining, solvent, and number of freeze-thaw cycles. Flexibility in the choice of fields displayed meant that we were also able to incorporate existing biological data, such as GI50 data from NCI’s human tumour cell line screen.”

“With the master library complete, tracking compounds to their final location on an assay plate is simply a matter of plate replication and reformatting. Commonly used reformatting techniques, such as combining four 96-well plates to create a 384-well daughter plate, can be stored as templates in the form of a csv file, and later invoked with ease by following a series of menus following the “create daughter plate” command. By tailoring the “plate format” folder, users can define the location of positive and negative controls, compound replicates, and compound concentrations to reflect actual assay formats used. Drop-down menus available in edit mode then make application of these formats to daughter plates particularly straightforward.”

“Plate management and compound tracking, however, is just the beginning of any high-throughput screening venture. The ultimate fate for almost every replicated plate, after all, is to be converted into a series of numbers representing either fluorescence polarisation, luminescence, or absorbance units, and each of these numbers in turn must then be interpreted for biological meaning. And it’s here, in the analysis of overwhelming volumes of raw data, where we have found BioAssay HTS to be most useful. Each assay is initially defined with a series of nested tables, starting with a raw data or ‘wells’ table.”

“Successive tables draw from values created in lower tables: for example, a wells table may subtract a background value, the next table may average wells of like concentration, and a third table may graph the averaged points along a sigmoidal dose-response curve. Once imported, the data can be examined at the level of any of these tables, from a z’factor for the entire run to the relative fluorescent units measured in well H1. In addition, information from any table can be displayed in plate or chart format, while user defined colour-coding allows for the rapid identification of either hits or invalid data points. Users can also view multiple plates side by side, or export the window contents to Excel with the click of a button.”

“We found the plate import template flexible enough to accommodate the output from almost any plate reader on the market, be it columnar or block, tab or space delimited, with one or many plates per file. The data import wizard guides the user through a brief series of steps connecting the raw data with the virtual assay plate or plates created in the plate library, after which the process is completely automatic.”

“No matter how impressive an array of liquid handlers, robot arms, and plate readers a laboratory may possess, the paydirt invariably lies in the data. And whether motivated by the race for a cure, that edge in the marketplace, or simply by the chemists down the corridor, efficiency in its analysis is always a must. To this end, I consider BioAssay HTS a cornerstone of our highthroughput screening effort, an invaluable asset and tool.”

CambridgeSoft laboratory software solutions are supplied and supported in the UK by Adept Scientific plc, Amor Way, Letchworth, Herts. SG6 1ZA; telephone +44 (0) 203 695 7810, fax +44 (0) 203 695 7819, email info@alfasoft.com or see Adept’s World Wide Web site http://www.adeptscience.co.uk/. Adept Scientific is one of the world’s leading suppliers of software and hardware products for research, scientific, engineering and technical applications on desktop computers.

With offices in the UK, USA, Germany and throughout the Nordic region, Adept Scientific is one of the world’s leading suppliers of software and hardware products for research, scientific, engineering and technical applications on desktop computers.

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