iMotifs

iMotifs – sequence motif editor for the Mac

iMotifs is a powerful yet easy to use sequence motif viewer and editor for the Apple Mac computers (Leopard or later). iMotifs is a research tool for computational biologists that allows viewing, editing and analysing XMS formatted sequence motif set files (position weight matrices).

Read the Getting Started with iMotifs guide for basic usage instructions.
Download iMotifs Version 0.2.5 from http://github.com/mz2/imotifs/downloads.


Installation: double-click the downloaded DMG package in Finder and drag to Applications.

(this Post content was reproduced from: http://wiki.github.com/mz2/imotifs/, Via Bioinformatics Advance Access.)

FileMaker Pro Custom Functions

Brian Dunning web-site: a Great resource to find custom functions for FileMaker (©FileMaker Inc, Advanced-version only)

Search for a Custom Function:



Free library of FileMaker Pro Custom Functions

you will be re-directed to Brian Dunning's site

(this Post content was reproduced from: http://www.briandunning.com/filemaker-custom-functions/recentlist.php)

Head in the clouds

It seems that due to my recent post, Bioinformatics and cloud computing, I have been labeled a cloud skeptic. While I don’t reject that label outright, I won’t accept it either. If I may label myself, I would call myself a cloud realist. My first piece of evidence is that at the end of my previous post I specifically state, “This is all not to say that there is not a place for cloud and other distributed computing frameworks in bioinformatics, but that’s the topic of a future post.” Unfortunately, this is not the future post to which that statement refers. The purpose of this post is to respond to some of the comments made on that post and around the web.

read more on the original page

(this Post content was reproduced from: http://www.politigenomics.com/2010/01/head-in-the-clouds.html#comments, Via PolITiGenomics.)

Up in a cloud?

Up in a cloud?
Nature Biotechnology 28, 13 (2010). doi:10.1038/nbt0110-13
Author: Clare Sansom
Cloud computing offers solutions for companies wrestling with large-scale data sets, but security issues will likely continue to restrict its use to precompetitive or nonconfidential data. Clare Sansom reports.

(this Post content was reproduced from: http://feeds.nature.com/~r/nbt/rss/current/~3/PJhwOkO_UqA/nbt0110-13, Via Nature Biotechnology.)

The Best of Bitesize Bio 2009

Before we get our brains fully back into gear after the festive season and embark on what we hope will be a momentous year for Bitesize Bio (watch this space, we’ve got some cool stuff in store), we thought this would be a good time to look back at the best articles we published in 2009.

Below are the 10 most popular articles that were published in the last year. Enjoy.

1. Free Online Bioinformatics Tools – Carrie topped the chart with a great article describing 4 must-use, free bioinformatics resources.

2. How to Create a Heatmap in Excel – A neat Excel hack from Paul, showing how to bring your numerical results to life in glorious technicolor.

3. Quantitative RT-PCR: One-step or Two-step RT? – Shoba weighed in with some excellent practical advice for quantitative PCR

4. An Intro to Cell-free Protein synthesis – And Shoba wasn’t finished there — she also produced this excellent beginners guide to cell free protein synthesis.

5. Reasons to be a Scientist Part II – If you want to reassure yourself that science is a great career choice, have a look at this one.

6. Delivering Effective Criticism – This is a message for anyone who is or will be a supervisor in any capacity. Think about how you treat your charges!

7. Plasmid v Genomic DNA Extraction:The Difference – Another molecular biology mystery demystified by Suzanne

8. 5 Types of Bad Boss and How to Handle Them – And some great practical advice from Suzanne on how to deal with your bad boss.

9. How To Get Great DNA Sequencing Results – Because bad sequencing results are such a waste of time.

10. 10 Tips for Consistent Real-Time PCR - And not content with only two entries in the top 10, Shoba sneaks in a 3rd with this excellent tip sheet.

I hope that these will help your brain wake up for the new year. If you have any personal favorites, please share them in the comments.

As I said, look out for some more great stuff from us in the coming year. And if you want to be a part of it and join our writing team, the door (or, rather, the contact form) is always open.

Best of luck with your research in 2010.

(source URL, Via Bitesize Bio.)

CoLocalizer Pro 2.5.2

About CoLocalizer Pro A quantitative colocalization analysis software. It is used to obtain new and objective information about proteins and nucleic acids visualized using fluorescence techniques. CoLocalizer Pro combines the power of it’s unique background correction tools with implementation of already established algorithms to estimate colocalization quantitatively. CoLocalizer Pro software is used by leading scientific laboratories worldwide and has become a dé facto standard in this field of research. Many more features.

(source URL, Via Downloads - Mac OS X - Math & Science.)

jORCA: Easily integrating bioinformatics web services

Motivation: Web services technology is becoming the option of choice to deploy bioinformatics tools that are universally available. One of the major strengths of this approach is that it supports machine-to-machine interoperability over a network. However, a weakness of this approach is that various Web Services differ in their definition and invocation protocols, as well as their communication and data formats—and this presents a barrier to service interoperability.

Results: jORCA is a desktop Client aimed at facilitating seamless integration of Web Services. It does so by making a uniform representation of the different web resources, supporting scalable service discovery, and automatic composition of workflows. Usability is at the top of the jORCA agenda; thus it is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users.

Availability and Implementation: jORCA binaries and extended documentation are freely available at http://www.bitlab-es.com/jorca under the Creative Commons Attribution-No Derivative Works 2.5 Spain License and jORCA source code (implemented in Java) is available under request. (GPL v3 license). jORCA has been tested under UNIX (Fedora 11, open SUSE 11 and Ubuntu 8.1), MS-Windows and Mac OS 10.5 operating systems. Java VM version 1.6 o later is required.

Contact: ots@uma.es, vickymr@uma.es

(source URL, Via Bioinformatics - Advance Access.)