Storage and retrieval of microarray data and open source microarray database software.

Mol Biotechnol. 2005 Jul; 30(3): 239-51
Sherlock G, Ball CA

Microarray technology has been widely adopted by researchers who use both home-made microarrays and microarrays purchased from commercial vendors. Associated with the adoption of this technology has been a deluge of complex data, both from the microarrays themselves, and also in the form of associated meta data, such as gene annotation information, the properties and treatment of biological samples, and the data transformation and analysis steps taken downstream. In addition, standards for annotation and data exchange have been proposed, and are now being adopted by journals and funding agencies alike. The coupling of large quantities of complex data with extensive and complex standards require all but the most small-scale of microarray users to have access to a robust and scaleable database with various tools. In this review, we discuss some of the desirable properties of such a database, and look at the features of several freely available alternatives.

See original: HubMed - "open source"[ti] review[pt] Storage and retrieval of microarray data and open source microarray database software.

Mobile genetic elements: the agents of open source evolution.

Nat Rev Microbiol. 2005 Sep; 3(9): 722-32
Frost LS, Leplae R, Summers AO, Toussaint A

Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.

See original: HubMed - "open source"[ti] review[pt] Mobile genetic elements: the agents of open source evolution.

Optimizing the use of open-source software applications in drug discovery.

Drug Discov Today. 2006 Feb; 11(3-4): 127-32
Geldenhuys WJ, Gaasch KE, Watson M, Allen DD, Van der Schyf CJ

Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process. Among the reviewed software programs are applications programmed in JAVA, Perl and Python, as well as resources including software libraries. These programs might be useful for cheminformatics approaches to drug discovery, including QSAR studies, energy minimization and docking studies in drug design endeavors. Furthermore, this review explores options for integrating available computer modeling open-source software applications in drug discovery programs.

See original: HubMed - "open source"[ti] review[pt] Optimizing the use of open-source software applications in drug discovery.

Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.

Curr Pharm Des. 2006; 12(17): 2111-20
Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL

The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software.

See original: HubMed - "open source"[ti] review[pt] Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.

Open source tools and toolkits for bioinformatics: significance, and where are we?

Brief Bioinform. 2006 Sep; 7(3): 287-96
Stajich JE, Lapp H

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

See original: HubMed - "open source"[ti] review[pt] Open source tools and toolkits for bioinformatics: significance, and where are we?

Can open-source R&D reinvigorate drug research?

Nat Rev Drug Discov. 2006 Sep; 5(9): 723-9
Munos B

The low number of novel therapeutics approved by the US FDA in recent years continues to cause great concern about productivity and declining innovation. Can open-source drug research and development, using principles pioneered by the highly successful open-source software movement, help revive the industry?

See original: HubMed - "open source"[ti] review[pt] Can open-source R&D reinvigorate drug research?

Bioconductor: an open source framework for bioinformatics and computational biology.

Methods Enzymol. 2006; 411: 119-34
Reimers M, Carey VJ

This chapter describes the Bioconductor project and details of its open source facilities for analysis of microarray and other high-throughput biological experiments. Particular attention is paid to concepts of container and workflow design, connections of biological metadata to statistical analysis products, support for statistical quality assessment, and calibration of inference uncertainty measures when tens of thousands of simultaneous statistical tests are performed.

See original: HubMed - "open source"[ti] review[pt] Bioconductor: an open source framework for bioinformatics and computational biology.

Open-source software for radiologists: a primer.

Clin Radiol. 2007 Feb; 62(2): 120-30
Scarsbrook AF

There is a wide variety of free (open-source) software available via the Internet which may be of interest to radiologists. This article will explore the use of open-source software in radiology to help streamline academic workflow and improve general efficiency and effectiveness by highlighting a number of the most useful applications currently available. These include really simple syndication applications, e-mail management, spreadsheet, word processing, database and presentation packages, as well as image and video editing software. How to incorporate this software into radiological practice will also be discussed.

See original: HubMed - "open source"[ti] review[pt] Open-source software for radiologists: a primer.

Open-source tools for immersive environmental visualization.

IEEE Comput Graph Appl. 2007 Mar-Apr; 27(2): 88-91
Sherman WR, Su S, McDonald PA, Mu Y, Harris F

See original: HubMed - "open source"[ti] review[pt] Open-source tools for immersive environmental visualization.

Open-source software opportunities and challenges.

J Am Coll Radiol. 2006 Jan; 3(1): 14-5
Harrington DP

See original: HubMed - "open source"[ti] review[pt] Open-source software opportunities and challenges.

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group.

Brief Bioinform. 2008 Jan; 9(1): 69-74
Mooney SD, Baenziger PH

A common challenge for bioinformaticians, in either academic or industry laboratory environments, is providing informatic solutions via the Internet or through a web browser. Recently, the open source community began developing tools for building and maintaining web applications for many disciplines. These content management systems (CMS) provide many of the basic needs of an informatics group, whether in a small company, a group within a larger organisation or an academic laboratory. These tools aid in managing software development, website development, document development, course development, datasets, collaborations and customers. Since many of these tools are extensible, they can be developed to support other research-specific activities, such as handling large biomedical datasets or deploying bioanalytic tools. In this review of open source website management tools, the basic features of content management systems are discussed along with commonly used open source software. Additionally, some examples of their use in biomedical research are given.

See original: HubMed - "open source"[ti] review[pt] Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group.

Chemical Descriptors Library (CDL): a generic, open source software library for chemical informatics.

J Chem Inf Model. 2008 Oct; 48(10): 1931-42
Sykora VJ, Leahy DE

In this article the Chemical Descriptors Library (CDL), a generic, open source software library for chemical informatics is introduced. The library is written using standard-compliant C++ programming language. The CDL provides a generic interface for traversing the structure of a molecular graph and accessing its properties. As a result, the software offers flexibility, reusability, and maintainability. This interface has been used to develop several chemical informatics algorithms, including molecular text format parsers and writers; substructure, pharmacophore, and atom type fingerprints; and both common substructure search and SMARTS search. The algorithms are described and evaluated on 3 data sets comprising 1000, 50000, and 100000 small molecules, respectively. The properties of the algorithms in terms of complexity analysis and processing times are presented and discussed.

See original: HubMed - "open source"[ti] review[pt] Chemical Descriptors Library (CDL): a generic, open source software library for chemical informatics.

Open source GIS for HIV/AIDS management.

Int J Health Geogr. 2008; 7: 53
Vanmeulebrouk B, Rivett U, Ricketts A, Loudon M

BACKGROUND: Reliable access to basic services can improve a community's resilience to HIV/AIDS. Accordingly, work is being done to upgrade the physical infrastructure in affected areas, often employing a strategy of decentralised service provision. Spatial characteristics are one of the major determinants in implementing services, even in the smaller municipal areas, and good quality spatial information is needed to inform decision making processes. However, limited funds, technical infrastructure and human resource capacity result in little or no access to spatial information for crucial infrastructure development decisions at local level.This research investigated whether it would be possible to develop a GIS for basic infrastructure planning and management at local level. Given the resource constraints of the local government context, particularly in small municipalities, it was decided that open source software should be used for the prototype system. RESULTS: The design and development of a prototype system illustrated that it is possible to develop an open source GIS system that can be used within the context of local information management. Usability tests show a high degree of usability for the system, which is important considering the heavy workload and high staff turnover that characterises local government in South Africa. Local infrastructure management stakeholders interviewed in a case study of a South African municipality see the potential for the use of GIS as a communication tool and are generally positive about the use of GIS for these purposes. They note security issues that may arise through the sharing of information, lack of skills and resource constraints as the major barriers to adoption. CONCLUSION: The case study shows that spatial information is an identified need at local level. Open source GIS software can be used to develop a system to provide local-level stakeholders with spatial information. However, the suitability of the technology is only a part of the system - there are wider information and management issues which need to be addressed before the implementation of a local-level GIS for infrastructure management can be successful.

See original: HubMed - "open source"[ti] review[pt] Open source GIS for HIV/AIDS management.

2009 December 11

2009 December 11



Messier Craters in Stereo Credit Apollo 11,
;

Stereo Image by
Patrick Vantuyne

Many bright nebulae and star clusters in planet Earth's sky
are associated with the name of
astronomer Charles Messier,
from his famous 18th century catalog.

His
name is also given
to these two large and remarkable craters
on the Moon.

Standouts in the dark, smooth lunar Sea of Fertility or Mare Fecunditatis,
Messier (left) and Messier A have dimensions of 15 by 8
and 16 by 11 kilometers respectively.

Their elongated shapes are explained by
an extremely shallow-angle trajectory followed by
the impactor, moving left to right,
that gouged out the craters.

The shallow impact also resulted in two
bright rays of material
extending along the surface to the right, beyond the picture.

Intended to be viewed with
red/blue glasses (red for the left eye),
this striking stereo picture of the crater pair was recently created
from high resolution scans of two images
(AS11-42-6304,
AS11-42-6305)
taken during the Apollo 11 mission to the moon.

light-weekend

This post has been generated by Page2RSS

See original: Astronomy Picture of the Day 2009 December 11

Unusual unapproved drug action by FDA against Provident Pharmaceuticals [Terra Sigillata]

In an article by Wayne Heilman of the Colorado Springs Gazette, I learned of a US FDA action against contract drug manufacturer Provident Pharmaceuticals. The company has been cited for good manufacturing practices (GMP) violations as well as the manufacture of unapproved drugs. The GMP violations are of a magnitude that FDA requested that Provident hire a GMP training consultant to bring the facility up to snuff.

However, Heilman seized upon an interesting side light in the warning: the names of the unapproved drugs apparently made by the company are missing from the detailed warning letter.

By unapproved drugs, FDA means drugs whose safety and efficacy has not been formally investigated under modern criteria. Some of these agents are those which the average person might say, "Really? That was never approved? You're kidding, right?"

I suspect this is an innocent omission - I hypothesize that Provident wasn't doing anything nefarious - because FDA has been widely aggressive in acting against companies marketing such old drugs, a topic that deserves its own post. In the meantime, the reader may care to visit this Unapproved Drugs site at fda.gov.

A good example is the expectorant, guaifenesin, a natural product isolated for trees of the Guaiacum genus. This compound, a racemic mixture actually, was approved by FDA in 1952 to increase the volume and reduce the viscosity of respiratory secretions. However, it was never formally approved after the 1962 legislation that gave the US most of its current guidelines for preclinical and clinical drug testing.

When FDA began its current enforcement campaign against unapproved drug manufacturers, Reckitt Benckiser seized upon guaifenesin being an unapproved drug, brought it up to modern standards, and now has a top-selling product with Mucinex, accompanied by those animated mucus blob characters that either charm or repulse.

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Also check out the featured ScienceBlog of the week: Neurotopia

See original: ScienceBlogs Select Unusual unapproved drug action by FDA against Provident Pharmaceuticals [Terra Sigillata]