A typical scientific article will require the use of several tools to reach its final published state. First, most researchers use Microsoft Word and Excel for text writing and tables. They also use EndNote to manage and create the bibliographies you will find in every scientific article. Finally, scientists use a graphics suite, such as Adobe's Photoshop, for figures and PDF creation. This software listing scales up to more than one thousand dollars. It's practically impossible for the regular student to purchase such a platform. In some laboratories, when the head researcher is kind enough, you will find a computer where most of these tools are installed and shared by all members of the team. But what if you could create your own open-source research writing box for free? In fact, you can. You can accomplish the entire array of tasks associated with scientific writing with any good Linux distribution.
Although OpenOffice.org can complete a fair portion of the job, it doesn't contain a bibliographic manager tool such as EndNote yet. Such a facility is necessary for academic writer and OpenOffice.org is supposed to fill the blank with some bibliographic extensions in its next version. For now, there is a commercial web-based tool called WriteNote which offers a 30 day free trial and enables you to produce a bibliography with RTF files created by OpenOffice.org.
Some of the LaTeX features include insertion of tables and figures as well as the capacity to create complex mathematical equations. Additionally, there are tremendous advantages in learning to write with LaTeX. In fact, BibTeX could get you out of proprietary software tomorrow. You can gather your bibliographic references in a simple text file with the BibTeX syntax and easily insert quotations inside your LaTeX documents, automatically generating a bibliography at the end of your articles.
While the LaTeX format requires a minimum of learning, you can rely on the useful TeXmed web-based tool to query NCBI PubMed and generate BibTeX entries for you. You must specify, in your LaTeX document, a bibliography style to format it according to the journal's recommendations. In fact, many journals now offer their bibliography style on their website. If you can't find the format that you need on the web, you can use custom-bib to create the style you need.
LyX is a GUI front end to LaTeX. Though it has its own file format, it can import and export to LaTeX. LyX looks like a word processor while taking care of all the formatting, just like LaTeX. LyX is fully featured and let you insert figures, tables, mathematical equations and more. Though managing a bibtex text file is very easy, you can rely on graphical tools here too. Software like gBib and JabRef will help you deal with your numerous references and even let you insert them in LyX, just like EndNote does with Word.
You also need to learn how to use new software. A few of the applications mentioned above only have a command-line interface, but most operations can be performed using GUI-based tools. There is plenty of documentation online, and you can always join an IRC channel to get live help. In a short time, you will become very functional, and you will reach new levels of productivity.
The worst drawback of using Linux in a Microsoft-based environment may involve compatibility issues with your coworkers. Since my boss insists on working with .doc files, I have to convert my papers to RTF using latex2rtf before I send him anything, even if PDF is the most portable format out there. But this doesn't stop me from benefiting of the LaTeX functionality.
Finally, you must rely on the Internet for support. Most of the system administrators in the research field don't know much about Linux (at least not in Quebec, where I'm working) and won't be able to support you if you have problems.
With little experience, you will start working faster and more efficiently. Serious page formatting issues found in Windows-based WYSIWYG software will be gone. Finally, you will be able to easily share your work by creating high quality PDF files.
An example screenshot of my desktop publishing environment can be seen here.
Database SoftwareThis is a new alpha development release, adding new features and fixing recently discovered bugs." explains events under MySQL version 5.1.6. "In this article, I'll give a preliminary description of a new MySQL feature for scheduling and executing tasks. In version 5.1.6, MySQL has added support for events. That is, you can now say: "I want the MySQL server to execute this SQL statement every day at 9:30am, until the end of the year" -- or anything similar that involves any number of SQL statements, and a schedule. Note that events are new and still in alpha, so there is still a good chance that we'll have to make adjustments as people experiment with them. This article describes the state of affairs only for the 5.1.6 release of MySQL."
Embedded SystemsBusyBox, a compressed collection of command line tools for embedded systems, has been released. "The new stable release is BusyBox 1.1.0. It has a number of improvements, including several new applets. (It also has a few rough spots, but we're trying out a "release early, release often" strategy to see how that works. Expect 1.1.1 sometime in March.)" KLone, a small embeddable web server, has been released. LinuxDevices.com is also running a review of KLone. (Thanks to Steven Dorigotti.)
Web Site DevelopmentVersion 2.4 is a major feature release."
Audio ApplicationsSilentJack is a silence/dead air detector for the Jack Audio Connection Kit. It monitors the peak levels on a single JACK input port, and checks to see if they are below a specified theshold. SilentJack then runs a command after silence has been detected for a given number of seconds. It then waits for the command the finish, and waits for a grace period before detecting silence again."
Data Visualizationhas been announced. "This release adds a new option to draw color gradients in the background, an enhanced perspective projection mode, a new "lasso" selection mode, a new snapping grid when adding points in the GUI, a new extrusion syntax and nicer normal smoothing. This release also contains various small bug fixes and enhancements."
ElectronicsCovered, a Verilog code coverage analysis tool, is available. "It has been almost a year since the last development release of Covered, but in the meantime there has been a lot of work put into the score command of Covered during this time to fix bugs, add more coverage support for various Verilog constructs, simulate more accurately, remove memory corruption/estrangement and improve the run-time speed of the score command. I think that user's of Covered will appreciate the enhancements. Documentation updates have been made and build problems have been fixed (Covered now compiles cleanly for Fedora Core 3 builds)." Kicad an electronic printed circuit board CAD package, is out with a bug fix and one new feature.
GUI Packageshas been announced. "This release candidate has been tested with fltk-1.1.6 and requires Python2.4." has been announced. "SPTK 3.0.12 adds support for the database driver messages. These messages may be sent to the driver by the database server on different occasions. These messages may include the extended error information, and the messages created by a stored procedure using (for MSSQL, for instance) PRINT statement."
Mail ClientsThunderbird 1.5 is out. Changes in this release include improvements to the automatic update system, smarter address auto-completion, on-the-fly spelling checking, better searching, some simple phishing detection (covered here last October), the ability to delete attachments, and much more; see the release notes for details. (As seen on MozillaZine)
Office ApplicationsBeagle Newsletter has been published. "Beagle is a search tool that ransacks your personal information space to find whatever you're looking for. Beagle can search in many different domains." has been announced. "The HylaFAX development team is pleased to announce our 4.2.5 patch level release! This fixes the problems users have been reporting in 4.2.4, which will be removed from the FTP and web sites. As always, our sincerest thanks go to all who participate and provide feedback." Several security fixes are included in this release.
Office Suiteswrites about the conversion of legacy documents to OO.o in an O'Reilly xml.com article. "Like its Microsoft counterpart, OpenOffice has a macro language. You can start up OpenOffice from the Linux or Windows command-line prompt with instructions to to run a particular macro, and you can even pass a filename as a parameter to that macro. Adding the -invisible switch to the command line tells OpenOffice to start up without the graphical user interface (GUI). Put all these together, and you've got a command line that converts a Microsoft Office file to an OpenOffice file (or an Acrobat file) with no use of the GUI. To convert a hundred files, you can use a Perl script or other scripting language to create a batch file or shell script that has the hundred commands necessary to convert those files."
Streaming Mediahas been announced. "Gst-Python provides Python bindings for the GStreamer project. These bindings provide access to almost all of the GStreamer C API through an object oriented Python API. This release allow fractions in structures and added vmethods for base classes. "
Web BrowsersThe minutes from the January 4, 2006 mozilla.org staff meeting have been announced. "Issues discussed include Upcoming Releases, Marketing, Thunderbird, 1.9 Roadmap, Firefox 2 Process and Calendar. The mintues have been posted to the new mozilla.dev.general newsgroup, which is accessible via news.mozilla.org."
Languages and Tools
Javaan article on J2EE exception handling. "One common hassle in J2EE development is exception handling: many apps devolve into a mess of inconsistent and unreliable handling of errors. In this article, ShriKant Vashishtha introduces a strategy for predictably collecting your exception handling in one place." shows how to interface Java to the PAM system in an IBM developerWorks article. "If you are a security developer and need to interface a Java application with the local operating system user registry, what do you do? This article gives you the answer: UNIX/Linux PAM (Pluggable Authentication Module)-compatible systems that use authentication based on the GNU MD5 extensions to the crypt() system call. I'll describe these extensions and show you a Java implementation of MD5 crypt (using FreeBSD as my UNIX)."
LispThis version adds new options to SOCKET-SERVER, changes the way a proxy can be specified for EXT:HTTP-PROXY, treats named pipes correctly, and fixes a few bugs." HEUTE (Hierarchical Extensible Unit Testing Environment for Common LISP) is a unit testing framework written in Common Lisp. It features a hierarchical approach to testing in which a test suite is represented by a CLOS class, with subclasses corresponding to sub-suites. A suite is considered passed only when its sub-suites also pass."
Perllooks at the motivation for designing Perl 6 in an O'Reilly article. "Perhaps the biggest imperfection of Perl 5 is its internals. Though much of the design is clever, there are also places of obsolescence and interdependence, as well as optimizations that no one remembers, but no one can delete without affecting too many other parts of the system. Refactoring an eleven-plus-year-old software project that runs on seventy-odd platforms and has to retain backwards compatibility with itself on many levels is daunting, and there are few people qualified to do it. It's also exceedingly difficult to recruit new people for such a task."
PHPVersion 4.4.2 of PHP has been announced. "This release address a few small security issues, and also corrects some regressions that occurred in PHP 4.4.1. All PHP 4 users are encouraged to upgrade to this release."
Also, development version 5.1.2 of PHP is out. "This release combines small feature enhancements with a fair number of bug fixes and addresses three security issues."
PythonpyPdf, a Python-based PDF toolkit, is out. Changes include a new page rotation capability, Improved PDF reading support and PDF 1.5 support.
RubyRuby Weekly News looks at the latest discussions from the ruby-talk mailing list.
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