Category: Software

Now you see it, now you don’t

Now here’s an experiment at removing those irritating lines and wires that make their way into every photo (especially those in cities). Having read about Snapheal CK, I bit the bullet and bought a copy of the license. And the results are below to compare. Snapheal makes removing lines, wires and other unwanted features from a picture a doddle. Interestingly enough, the algorithm underneath the hood does a brilliant job and understanding the background patterns so that there are no ghosts left from the removal! Of course, nothing is perfect and one shouldn’t expect miracles and nothing can rescue a badly composed photograph.

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The photos above are of Casa Bruno Cuadros (a famous umbrella shop in the La Rambla area of Barcelona), and show the photos before and after treatment with Snapheal CK.

Why Firefox is great for Bioinformatics ?

Firefox, the latest offering from the Mozilla Foundation is one of the best web browsers in the market at the moment. In addition to built-in extras like popup-blocking, tabbed browsing, smart searching capabilities, the Mozilla development platform offers more than 200 add-ons in the form of extensions.
According to the mozilla update site, the official download home for all extensions:

Extensions are small add-ons that add new functionality to your Mozilla program. They can add anything from a toolbar button to a completely new feature.

Firefox offers the average biologist many advantages over Internet Explorer or Opera. Warning:As the developer of one of the first bioinformatics extensions for Firefox, the case that I put forward below may be biased !!!

a) Bioinformatics Extensions: Search and Analysis

  • biobar – A power-browsing toolbar for searching over 40 biological databases. The complete list of databases than can be searched in given here. In addition, the toolbar offers a high degree of customisation, by allowing users to add their own databases to the toolbar. Biobar is available for the mozilla family of browsers including Firefox, Mozilla (1.4+) and Netscape 7+.
  • bioFOX -Code bioFOX aims at implementing various bioinformatics tools as an extension on Firefox. Analysis of your favorite gene(s) usually require(s) retrieving it from a database like NCBI or Swiss-Prot and then performing one or more tasks including translation, blast search, property analysis like codon usage, molecular weight calculation etc. bioFOX is available as a sidebar only for Firefox and can be activated by pressing Ctrl-shift-F after installation. The bioFOX homepage has more documentation.
  • BioMed Central Toolbar – BioMed Central has a toolbar available for both Mozilla/IE (Wonders!) which, much like biobar, allows a user to search BioMed Central, PubMed, Faculty of 1000 and Google. A similar search plugin is available for Firefox from the same site.
  • Athens Toolbar – This toolbar will be useful to people who use the Athens Authentication Service to access sites like Ingenta for full-text access to library subscription journals. Not very useful for people outside the UK.
  • LSID – The lsid extension enables resolution of lsidres URIs. The lsidres protocol is used by IBM’s LaunchPad for Life Sciencer Identifiers (LSIDs). At present, LauchPad is only available for Internet Explorer 6 running on Windows. This extension is a first step towards adding support for this protocol to other browsers.

b) Search Plugins: Quick Searches

Firefox comes built-in with a search box at the top-right edge of the browser. by default, the search plugins supported for that box are Google, Yahoo, Amazon, Dictionary, E-bay. However, it’s just as easy to add other search engines for this box. I have listed a few for Life Sciences below:

  1. NCBI Global – Search NCBI
  2. NCBI PubMed – Search Entrez
  3. HubMed – Search HubMed
  4. SwissProt – Search SwissProt

These and many others can be installed by a single click from Mycroft.

Other fantastic general purpose extensions include AdBlock a must to block all those unwanted banner ads, flash iframes etc.

Please let me know if the list is incomplete so that I can maintain a uptodate list for future reference.