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PyDaylight 1.0 released

July 24, 2005:

Dalke Scientific Software, LLC today announced the release of version 1.0 of PyDaylight package. PyDaylight is a rapid application development library for chemical informatics. Written for the Python programming langauge, it is based on the Daylight toolkit and adds high-level interfaces such as objects, exceptions, iterators, and depiction libraries. This release adds support for version 4.91 of the Daylight toolkit.

Says Andrew Dalke, founder of Dalke Scientific Software, "PyDaylight is a mature system with over 6 years of use in biotechs and pharmas. The code base only changes these days when the underlying toolkit changes so the '1.0' numbering is long since due."

[Release details]

"Daylight" and "Daylight toolkit" are registered trademarks of Daylight Chemical Information Systems, Inc. Daylight C.I.S. is neither affiliated with nor responsible for PyDaylight. All other marks are property of their respective owners.

EuroPython slides

July 11, 2004:

The slides from Andrew Dalke's presentation at the 2004 EuroPython conference in Göteborg are now available. They provide an overview of different Python libraries for computational chemistry and biology.

NBN slides available

April 11, 2004: Andrew Dalke of Dalke Scientific Software was asked by the National Bioinformatics Network of South Africa to teach a two-week course on introductory programming for bioinformatics using Python. It took place 2-14 Feb at NBN's site in Bellville, South Africa.

The class had nearly 30 people in it with backgrounds from college seniors to bioinformatics staff researchers, and programming experience ranging from none to several years. The course stepped through the basics of programming with many hand-on exercises, including some meant to be challenging to the more experienced people.

Said Dr. Dan Jacobson, head of the NBN, "the students enjoyed your course immensely and I am happy that you were able to give them such a good introduction to Python."

The slides for the course are now available.

If you would like us to teach a course in Python, Biopython, PyDaylight or related topics, please email us at info@dalkescientific.com.

PyCon 2004 talk available

April 9, 2004: Andrew Dalke presented the talk Python in Bioinformatics and Chemical Informatics March 26, 2004 at PyCon 2004 in Washington, DC.

Andrew accepted to the PSF

April 8, 2004: The Python Software Foundation formally announced today that Andrew Dalke of Dalke Scientific Software has been accepted as a nominated member.

PyRSS2Gen-0.0 released

September 6, 2003: Dalke Scientific Software, LLC made their first developer release of PyRSS2Gen, a Python library for generating RSS 2.0 feeds.

EUtils-1.0b1 released

January 12, 2003: Dalke Scientific Software, LLC today announced the release of their EUtils client for the Entrez databases at NCBI, including PubMed and GenBank. Written for the Python programming language, this package makes it easy to write programs which query the database, retrieve records, and get information about related records.

PyDaylight-0.85 released

August 25, 2002: Dalke Scientific Software, LLC today announced the release of version 0.85 of their PyDaylight package. "The previous release focused on improving the ease of installation," said founder Andrew Dalke. "We got great feedback on that, and now we've returned to filling out support for the Daylight toolkit. Most notably we added fingerprint support, which was our most frequently requested feature. In addition, for those writing GUIs, we improved depiction support and included an interface to Trolltech's Qt library."

BOSC 2002 presentations available

August 6, 2002: The two presentations by Andrew Dalke for last week's BOSC (Bioinformatics Open Source Conference) are now available. The main talk introduces the field of software usability, including some of the special advantages and problems of making open source bioinformatics software more usable. The second is a lightning talk on the flat-file indexing specification.

Dalke Scientific at BOSC and ISMB 2002

July 2002: Andrew Dalke will be at BOSC and ISMB next month. In addition to being an organizer of the BOSC conference he will be presenting a talk on usability in bioinformatics software and why it's important and a lightning talk on the new Open Bioinformatics Foundation flat-file indexing specification

O'Reilly conference presentations available

February 4, 2002: The three presentations by Andrew Dalke for last week's O'Reilly Bioinformatics Technology Conference are now available. The two main talks are titled "Biopython" and "Martel, Parsing, and Bioformats" and cover two of the core technologies developed by Dalke Scientific Software. The third presentation is a lightning talk titled "A Plea for Paranoia" and describes why defensive programming is needed and how to make safer software.

Essay opposing the OpenInformatics petition

January 14, 2002: Andrew Dalke's essay titled "Why I'm Not Supporting the Open Informatics Petition" was published today on the O'Reilly Network. Dalke Scientific Software is a strong supporters of open-source software but believe the petition, which wants to require that all government funded academic software be released under an Open Source license, will hinder scientific development and will not achieve its aims of ready access to source code for non-profit purposes. The petition is available from OpenInformatics.org. Andrew also wrote a clarifiation essay describing his interpretation of open source.

Biohackathon attendees announced

October 16, 2001: Yesterday Electric Genetics and O'Reilly & Associates announced their selection of Andrew Dalke, Jeff Chang, and Brad Chapman as attendees of the invitation-only Open Source Bioinformatics Hackathon. Andrew and Jeff started the Biopython project and all three are associated with Dalke Scientific Software.

New PyDaylight release available

October 15, 2001: Dalke Scientific Software today announced the release of version 0.8 of their PyDaylight package. PyDaylight is a rapid application development library for chemical informatics.

Andrew Dalke elected OBF Secretary

September 30, 2001: Today Andrew Dalke was elected Secretary of the Open Bioinformatics Foundation (OBF). The Open Bioinformatics Foundation is an umbrella group for the various Bio*.org projects that grew out of the original BioPerl project. The goal of the foundation is to provide financial, administrative and technical assistance for our various open source life science projects and the Bioinformatics Open Source Conference.

Commercial Support for Biopython

Copenhagen, July 17, 2001: Andrew Dalke announced at BOSC this morning that his company, Dalke Scientific Software, now provides commercial consulting and support services for Biopython. Biopython is an international collaboration to collect and produce open source bioinformatics tools written in the Python programming language.

Meet us at BOSC and ISMB

July 2001: Dalke Scientific and several of its partners will be at BOSC and ISMB. Come meet us and learn more about what we are doing with Biopython.

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