Andrew Dalke's Dairy archive

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Andrew Dalke's Dairy archive

Archive entries by year

All diary entries, from oldest to newest

Thu 2003/09/04 How much data at EBI?
Wed 2003/09/03 Distributing bioinformatics data sets using BitTorrent
Thu 2003/09/04 URIs for bioinformatics records
Fri 2003/09/05 Lincoln on SOAP, CORBA, and REST
Sat 2003/09/06 Site changes
Sat 2003/09/06 RSS for bioinformatics
Sat 2003/09/20 Ruminations about DAS2
Sat 2003/09/20 RSS feed up and running
Sun 2003/09/21 connection matrix vs. node with edges for molecules
Sun 2003/09/21 interactive Python shell
Mon 2003/09/22 Visual dataflow programming
Sat 2003/09/27 PythonCard and Boa Constructor not ready yet
Sun 2003/09/28 Tonight's Star Party
Mon 2003/09/29 Sequence Numberings
Mon 2003/10/06 Drawing molecules
Tue 2003/10/07 Exceptions to the graph model
Tue 2003/10/07 Naming molecules
Tue 2003/10/07 Naming known molecules
Wed 2003/10/08 Naming novel molecules
Tue 2003/10/14 Molecular Formula - History of Chemical Nomenclature
Tue 2003/10/14 Systematic Name - History of Chemical Nomenclature
Tue 2003/10/14 Paper databases -- History of Chemical Nomenclature
Wed 2003/10/15 WLN -- History of Chemical Nomenclature
Wed 2003/10/15 Computers -- History of Chemical Nomenclature
Sat 2004/01/03 Chemical Informatics Toolkits
Mon 2004/01/05 SMILES tokens
Wed 2004/04/07 Landvetter airport to Gothenburg and back again
Wed 2004/04/07 Site updated
Mon 2004/04/12 Parsing - oh the humanity.
Wed 2004/04/14 SDI, soft power, and gas != WMD
Sun 2004/05/02 CPU power vs. bandwidth
Tue 2004/12/07 Updated PyRSS2Gen
Sun 2004/12/12 Combinitorial Library Generation with SMILES
Mon 2004/12/27 Martel and Mindy status
Wed 2005/03/02 Faster fingerprint substructure tests
Sun 2005/04/10 Wrapping Dragon
Mon 2005/04/11 I590 slides available
Tue 2005/04/12 Wrapping command-line programs
Fri 2005/04/15 Wrapping command-line programs, part II
Sun 2005/04/17 Wrapping command-line programs, part III
Mon 2005/04/18 Wrapping command-line programs, part IV
Mon 2005/04/18 Wrapping command-line programs, part V
Wed 2005/04/20 Tracing python code
Thu 2005/04/21 Using XML-RPC
Thu 2005/04/21 Screen scraping
Fri 2005/04/22 Recent essays
Fri 2005/04/22 Parsing
Fri 2005/04/22 statistics
Fri 2005/04/22 matplotlib
Sat 2005/04/23 matplotlib without a GUI
Sun 2005/04/24 Interactive HTML
Sun 2005/04/24 HTML Templates
Tue 2005/04/26 CherryPy
Tue 2005/04/26 Web applications
Tue 2005/04/26 databases
Tue 2005/04/26 Extending Python
Sat 2005/05/07 Attachment points
Wed 2005/05/18 Updated ReseekFile
Wed 2005/05/18 Moving to Sweden
Thu 2005/06/02 urllib2 and HTTP authentication
Sun 2005/07/24 PyDaylight 1.0 released
Fri 2005/09/30 NBN lectures
Fri 2005/09/30 Using EUtils
Thu 2005/10/06 PyJudy-1.0
Sun 2006/03/19 Class instantiation performance
Mon 2006/03/20 Performance tuning
Wed 2006/03/22 File parsing locations
Tue 2006/08/22 PyProtocols for output generation
Wed 2006/08/23 with statement
Wed 2006/08/23 Building an ElementTree using with statments
Mon 2006/08/28 Levels of abstraction
Tue 2006/08/29 Parser Generators and Decorators
Wed 2006/08/30 GardenSnake language
Thu 2006/09/07 Simple lazy dependencies
Fri 2006/09/22 Slides for "Useful and New Modules" talk
Mon 2006/10/02 Added examples of Python calling C
Thu 2006/10/12 NBN notes
Tue 2006/10/24 XML-RPC in TurboGears
Mon 2006/11/06 IterParseFilter
Wed 2007/05/23 Administrative trivia
Wed 2007/05/23 OE8BitImage to PNG
Fri 2007/06/01 LOLPython
Mon 2007/06/25 Parsing SMILES, compression, Ragel
Wed 2007/07/25 Blogs a-hoy!
Thu 2007/07/26 Re: "Gzip for Molecular Similarity"
Thu 2007/07/26 Connection negotiation
Fri 2007/07/27 Structure viewer demo
Fri 2007/08/17 Kata and practice
Sun 2007/10/07 Wide Finder
Wed 2007/10/10 other Wide Finder implementations
Thu 2007/10/18 Resolver
Tue 2007/10/30 OpenSMILES
Tue 2007/10/30 Parser generators and SMILES
Tue 2007/10/30 Calculating MW with ANTLR
Thu 2007/11/01 ANTLR rules
Sat 2007/11/03 more ANTLR - Java, and comparisons to PLY and PyParsing
Sun 2007/11/11 Poster text for the German Conference on Chemoinformatics
Thu 2007/11/29 World's Greatest Authority
Fri 2007/11/30 OpenSMILES and aromaticity
Mon 2007/12/03 Time capsule
Thu 2007/12/20 Installing Linux
Sun 2007/12/23 Log analysis of my website
Mon 2008/03/03 Restricted python
Sun 2008/03/09 python4ply
Sun 2008/03/09 python4ply tutorial, part 1
Sun 2008/03/09 python4ply tutorial, part 2
Mon 2008/03/10 python4ply tutorial, part 3
Mon 2008/05/12 EuroCUP 2008 presentation
Thu 2008/06/26 Molecular fingerprints, background
Fri 2008/06/27 Generating molecular fingerprints with OpenBabel
Fri 2008/06/27 Computing Tanimoto scores, quickly
Sat 2008/06/28 Block Tanimoto calculations
Tue 2008/07/01 Faster block Tanimoto calculations
Thu 2008/07/03 HAKMEM 169 and other popcount implementations
Sat 2008/07/05 Testing the bitslice algorithm for popcount
Wed 2008/07/23 Teaching Python programming for cheminformatics
Fri 2008/08/08 Read 0 bytes, run out of memory
Sat 2008/09/20 EuroQSAR posters
Thu 2008/11/06 Teaching Python for cheminformatics
Tue 2008/11/11 Open source != peer review
Wed 2009/03/25 Python for Cheminformatics Training in Leipzig, 27-29 April
Fri 2009/03/27 Python 0.9.1p1
Tue 2009/09/15 100,000 tasklets: Stackless and Go
Sun 2009/11/15 100,000 tasklets: Stackless and Go
Fri 2009/12/04 DNS pre-resolution
Wed 2009/12/16 License agreements and usability
Tue 2009/12/29 Problems with TDD
Mon 2010/01/04 Content-Disposition bug in browsers?
Mon 2010/01/11 Fingerprint File Format
Wed 2010/01/20 Cheminformatics, bioinformatics, and system biology positions available
Sat 2010/01/30 Project hosting options?
Thu 2010/02/04 New Cheminformatics Projects
Mon 2010/02/22 Instrumenting the AST
Tue 2010/03/16 KNIME and beginners
Tue 2010/03/23 Upcoming cheminformatics programming training courses
Wed 2010/04/07 GothPyCon 2010
Mon 2010/04/12 How to compile openCHORD on a Mac
Tue 2010/04/27 Leipzig outline and flyer
Sun 2010/10/03 cyclops_mysql and jquery-marvin
Sat 2010/11/13 Ontologies of Algorithm Implementations
Sat 2010/12/18 What's the name of my field?
Sat 2010/12/18 Python and Django courses for cheminformatics
Tue 2010/12/28 Reordering SMILES atom order
Mon 2011/01/10 Subgraph enumeration
Thu 2011/01/13 Faster Subgraph enumeration
Sun 2011/01/16 Screening Teaser
Thu 2011/01/20 Implementing the CACTVS/PubChem substructure keys
Thu 2011/02/24 Work in a Swedish company? Self-employed American in Sweden needs your helps
Mon 2011/05/30 chemfp-1.0a1
Sat 2011/06/04 Dealing with SSSR
Sun 2011/06/05 Molecular Coding
Tue 2011/07/12 Code review
Tue 2011/07/12 Where free software and peer-review software differ
Wed 2011/11/02 Update: Faster population counts
Wed 2011/11/09 f2pypy
Mon 2011/11/14 Floats and doubles
Fri 2011/12/23 Inverted index using Python sets
Sun 2011/12/25 Unique fragments in PubChem
Tue 2012/01/03 ECFP-like fragments in PubChem
Fri 2012/01/13 OpenMP vs. POSIX threads
Mon 2012/01/16 My views on OpenMP
Tue 2012/01/17 I parallelize an algorithm
Thu 2012/01/19 Python's concurrent.futures
Sat 2012/05/12 MCS background
Sun 2012/05/13 fmcs - find the MCS of a set of compounds
Sun 2012/05/13 Finding the MCSes for the ChEBI ontology
Fri 2012/05/18 Topologically non-planar compounds
Mon 2012/05/21 Testing hard algorithms
Sun 2012/06/10 In search of an inverted index library
Mon 2012/06/11 Optimizing substructure keys
Tue 2012/08/21 The Structure Query Collection
Mon 2012/08/27 PyRSS2Gen for Python3
Sat 2012/11/10 Interview with Igor Filippov about OSRA
Thu 2012/12/13 Is TDD better than Apps Hungarian?
Sat 2013/07/27 Varkony Reconsidered
Tue 2014/06/17 8-bit SMILES
Thu 2014/06/19 Calvin Mooers
Sun 2014/07/06 The origin of the connection table
Wed 2014/07/09 chemfp's FPB format
Thu 2014/07/10 PNG checksum
Sat 2014/07/12 I/O location and error handling
Thu 2014/07/24 Lausanne Cheminformatics workshop and contest
Tue 2014/09/23 Summary of the /etc/passwd reader API
Wed 2014/09/24 New chemfp APIs
Thu 2014/09/25 chemfp's parse_molecule()
Fri 2014/09/26 chemfp's format API
Fri 2014/10/17 MACCS key 44
Thu 2014/11/27 MACCS in RDKit and Open Babel
Fri 2014/11/28 Indexing ChEMBL for chemistry search
Fri 2014/11/28 Similarity web service
Mon 2016/03/28 Fun with SMILES I: Does an element exist?
Wed 2016/08/03 Reading ASCII file in Python3.5 is 2-3x faster as bytes than string
Mon 2016/08/08 Molecular fragments, R-groups, and functional groups
Tue 2016/08/09 Fragment achiral molecules in RDKit using low-level functions
Sun 2016/08/14 Fragment chiral molecules in RDKit using low-level functions
Mon 2016/08/15 Faster parity calculation
Wed 2016/08/17 Use FragmentOnBonds to fragment a molecule in RDKit
Thu 2016/08/18 Software mentioned in ChEMBL SD records
Tue 2016/08/23 Fragment by copy and trim
Fri 2016/12/02 Weininger's Realization
Mon 2017/03/20 Fingerprint set similarity
Fri 2017/03/24 ChEMBL bioactivity data
Mon 2017/03/27 ChEMBL target sets association network
Mon 2018/06/04 mmpdb paper, poster, and walkthrough
Thu 2019/10/03 mmpdb crowdfunding consortium
Thu 2020/09/03 New chemfp licensing model in chemfp 3.4
Thu 2020/09/03 What's up with chemfp 1.x?
Tue 2020/09/08 Patents and molecular similarity
Tue 2020/09/08 Drug control law and molecular similarity
Thu 2020/09/10 United States v. Brown ... v. Tanimoto
Fri 2020/09/11 Similarity principle in legal cases
Mon 2020/09/14 Similarity principle variations
Tue 2020/09/15 Changes in chemfp 3.4
Tue 2020/09/15 chemfp on the command-line
Wed 2020/09/16 Faster gzip reading in Python
Thu 2020/09/17 SDF record walkthrough
Fri 2020/09/18 Handling the SDF record delimiter
Mon 2020/09/21 Molfile "S SKP"
Tue 2020/09/22 Fun with SDF records - chemfp's text toolkit
Wed 2020/09/23 Extracting two SDF data items with chemfp's text toolkit
Thu 2020/09/24 chemfp's chemistry toolkit I/O API
Fri 2020/09/25 Mixing text and chemistry toolkits
Mon 2020/09/28 Simple FPS fingerprint similarity search: variations on a theme
Tue 2020/09/29 Simple k-NN FPS Tanimoto and cosine similarity search
Wed 2020/09/30 Simple in-memory ChEMBL similarity search
Thu 2020/10/01 Simple BitBound ChEMBL similarity search
Fri 2020/10/02 Using RDKit BulkTanimotoSimilarity
Mon 2020/10/05 Faster in-memory ChEMBL search by using more C
Tue 2020/10/06 Faster BitBound ChEMBL search by using more C
Wed 2020/10/07 Even faster in-memory search with intersection popcount
Thu 2020/10/08 Cache and reuse popcount-sorted ChEMBL fingerprints
Fri 2020/10/09 A molfile precursor?
Mon 2021/02/15 Are 32-bit floats enough for your Tanimoto scores?