Blog Archive 2014 Managing your Biological Data with Python: a review Oct 20 2014 PacktPub new campaign Sep 29 2014 Packt Publishing offer Jul 03 2014 2013 Packt Publishing 50% off Oct 16 2013 Alternative way of installing Circos on OS X Aug 14 2013 Instant Django 1.5 Application Development Starter, a review May 07 2013 Circos Data Visualization How-to: a review Jan 10 2013 2012 Installing Circos on OS X Jun 03 2012 New blog Apr 09 2012 2011 Scientists are human beings Feb 23 2011 A plea to mankind, news outlets and even scientists Feb 16 2011 There are idiots everywhere … Feb 15 2011 Bioconductor Feb 10 2011 There’s dumb, and there’s … Feb 09 2011 What’s more important: the publication or the product? The publication. Feb 09 2011 Books 2011 Jan 24 2011 It’s s$@t like this, scientists Jan 16 2011 2010 I’ve failed Dec 31 2010 Question Dec 16 2010 Brazil, the country of the future. Always. Dec 16 2010 Books 2010 Dec 16 2010 Best and worst of 2010 Dec 13 2010 Of course I agree, Cytoscape Dec 08 2010 Interview with Rosie Redfield Dec 07 2010 You’re quite wrong, NASA Dec 07 2010 Secure OS Dec 06 2010 The new “form” of life and the Generation Mendeley Dec 05 2010 Preview of Best and Worst of 2010 Dec 02 2010 Why I left Biostar Dec 01 2010 Why I left Biostar, but I still like Stackoverflow Dec 01 2010 Help me with this one Nov 29 2010 Milking research papers, or recurrences of the same topic Nov 26 2010 11:11, November 11th Nov 11 2010 Zotero: now we’re talking Sep 22 2010 A positive note Sep 17 2010 A short list of things I don’t like about Mendeley Sep 17 2010 PLoS Blogs: I’m excited Sep 02 2010 Mendeley open-source: possible revenue streams Aug 28 2010 Campaign: We’re open, Mendeley Aug 27 2010 Why it makes sense, re: Mendeley open source Aug 27 2010 Mendeley is going to be open source Aug 27 2010 The rise and fall of software, sites and companies Aug 25 2010 Mendeley’s side Aug 24 2010 The Web’s Future Aug 24 2010 There’s still hope Aug 21 2010 One round of applause Aug 20 2010 Note to self, re:API or who said Mendeley didn’t teach me something? Aug 12 2010 Damn, Mendeley! Aug 09 2010 Gates and fountains, more Pepsi Jul 28 2010 My take on the future scientific blog community (long post) Jul 23 2010 More Pepsi for everyone … Jul 22 2010 I Jul 22 2010 World Cup 2010, final impression Jul 12 2010 Safari 5: the worst Jun 26 2010 2010 World Cup: second impressions Jun 26 2010 Bad street cred Jun 25 2010 2010 World Cup: first impressions Jun 14 2010 Publishing on Nature Jun 08 2010 Thank the Lord it’s Friday! Jun 04 2010 The problem with paid software, part 64563, support Jun 02 2010 Preview of Django 1.1 Testing and Debugging May 20 2010 I live in “the” Canada May 02 2010 Initial impressions about Bioinformatics Programming using Python May 01 2010 Do you think Bush was a bad president? Think again … Apr 30 2010 Scary Apr 28 2010 Python for Bioinformatics by Sebastian Bassi: a (short) review Apr 19 2010 Biostar: bioinformatics community Apr 17 2010 Repent sinners Apr 15 2010 The real value of blogging Apr 10 2010 Google Wave, part 64334533.08 Apr 09 2010 Bioinformatics needs investment II Apr 08 2010 Bioinformatics needs investment Apr 07 2010 Open Science and pregnancy Apr 06 2010 Paid software vs. donating Apr 04 2010 BPB on Github Apr 01 2010 Draft blog posts Apr 01 2010 I thought I was alone, but then I found another light Mar 30 2010 Earth hour Mar 26 2010 Python Testing Beginner’s Guide, review Mar 03 2010 Preview of Python Testing Beginner’s Guide Feb 22 2010 Preview of Python Testing Beginner’s Guide Feb 22 2010 If we tell you to Buzz … Feb 20 2010 I don’t understand the US Feb 19 2010 Do you deny Climate Change (nee Global Warming)? Feb 19 2010 Intelligent design? Feb 19 2010 Please stop … Feb 19 2010 London 2012, Vancouver 2010 Feb 18 2010 Google Wave and Buzz Feb 17 2010 That’s basically it Feb 15 2010 Palin Feb 07 2010 Laboratory Walkover: a pitch for a TV show Feb 06 2010 It’s really strange or why the iPad? Jan 28 2010 Something is not open at PLoS, maybe … Jan 28 2010 iPad is excellent!!! Jan 28 2010 Microsoft is more detrimental to Science, than the lack of Open Science, … Jan 28 2010 Feynman and me Jan 27 2010 Never understood Jan 25 2010 Thanks Conan! Jan 23 2010 Stay away Jan 22 2010 Premium Jan 20 2010 Why I won’t watch Avatar (or at least pay for) Jan 19 2010 I’m with Coco Jan 14 2010 Memories Jan 10 2010 Books 2010 Jan 10 2010 Phrase of the day Jan 04 2010 Preliminary review of Python for Bioinformatics by Sebastian Bassi Jan 03 2010 Lies, lies and even more lies Jan 02 2010 365 in 365 Jan 01 2010 2009 Best of the decade Dec 30 2009 2009 in review Dec 19 2009 Open Science/Access challenge Nov 30 2009 DIALIGN-TX has all the problems with scientific software Nov 26 2009 Google Wave invite: who wants one? Oct 01 2009 Mendeley’s PR machine and more Sep 30 2009 This is when I say farewell … Sep 28 2009 Books 2009 Aug 30 2009 Wave test Aug 21 2009 The best analogy for the FriendFeed purchase Aug 11 2009 What we learned last week: August 10th edition Aug 10 2009 Paper of the week: INDELible: A Flexible Simulator of Biological Sequence Evolution Aug 10 2009 Paper of the week: A Quick Guide to Organizing Computational Biology Projects Aug 03 2009 Movies 2009 Aug 03 2009 You should live there for sometime Jul 13 2009 It’s when I struggle to stay alive, or another Mendeley review Jul 13 2009 So you want to cover the next conferece via social media? Jun 03 2009 Internet “democracy” May 21 2009 Doing more harm than good May 13 2009 The new America’s cult May 12 2009 On anti-vaccine and the internet May 08 2009 It’s not just me, Victor. Apr 25 2009 Thanks, Jim! Apr 19 2009 This should not be here … or Notes to a bioinformatician - two years later Apr 17 2009 Mendeley: an extremely short review (sort of) Apr 03 2009 Phasing out scientific software Mar 31 2009 I haven’t joined Mendeley as community liaison Mar 18 2009 Presenting BioVB6 Mar 15 2009 BioPython and CVS Mar 13 2009 Why do I blog. Or: Science Blogging, is it worth? Feb 20 2009 Nostradamus? Feb 10 2009 On “join a startup” Feb 09 2009 BPforB is now PEP 8 compliant! Jan 31 2009 Why Open Science/Research won’t work, at least for now, a story from FriendFeed Jan 22 2009 Masterpieces Jan 07 2009 Cancer Research Blog Carnival #17 Jan 02 2009 2008 Best and Worst of 2008 Dec 20 2008 That’s it for 2008 Dec 19 2008 Restoring original fonts on Leopard (as long as you have TimeMachine) Dec 10 2008 Speechless Dec 07 2008 Why Open Science/Research won’t work, at least for now, a story from Google Reader Nov 21 2008 You may not know … Nov 20 2008 Poem Nov 19 2008 Creating an interface for the motif finding script, final Nov 19 2008 Creating an interface for the motif finding script, some corrections Nov 18 2008 The community comments on why Open Science/Research won’t work Nov 16 2008 The Science Blog Meme Nov 16 2008 Creating an interface for the motif finding script, part 8 Nov 13 2008 Why Open Science/Research won’t work (at least for now), first part of a long series Nov 13 2008 How to improve Science, in easy steps Nov 12 2008 Creating an interface for the motif finding script, part 7 Nov 11 2008 the 11th hour Nov 11 2008 Crooks Nov 07 2008 Software that I would never buy or use (even free) Nov 05 2008 Creating an interface for the motif finding script, part 6 Nov 04 2008 Motif finding interface on github Oct 30 2008 Creating an interface for the motif finding script, part 5 Oct 30 2008 Creating an interface for the motif finding script, part 4 Oct 29 2008 Creating an interface for the motif finding script, part 3 Oct 22 2008 Creating an interface for the motif finding script, part 2 Oct 21 2008 Creating an interface for the motif finding script, part 1 Oct 20 2008 I love spam!!! Sep 21 2008 Python, overepresented motifs, the Grand Finale Sep 05 2008 Obtaining overrepresented motifs in DNA sequences, final Sep 03 2008 Mendeley: a very short review Aug 25 2008 Obtaining overrepresented motifs in DNA sequences, part 13 Aug 20 2008 That should do it! Aug 20 2008 Business opportunities Aug 19 2008 Obtaining overrepresented motifs in DNA sequences, part 12.5 Aug 15 2008 Obtaining overrepresented motifs in DNA sequences, part 11 Aug 12 2008 These are really my sequences!! Jul 31 2008 Those are my sequences!! Jul 31 2008 Shame Jul 29 2008 Staring at the clouds Jul 23 2008 PLoS Computational Biology t-shirt Jul 08 2008 Bioinformatics career survey Jul 01 2008 What a happy day!! Jun 29 2008 Wordle Jun 18 2008 The “new” cult is coming to life Jun 14 2008 Chelsea Jun 11 2008 A quick assessment of factorial functions in Python Jun 06 2008 Poor octopi … Jun 04 2008 Obtaining overrepresented motifs in DNA sequences, part 10 Jun 04 2008 Obtaining overrepresented motifs in DNA sequences, part 9 Jun 03 2008 Obtaining overrerpresented motifs in DNA sequences, part 9 Jun 03 2008 Obtaining overrepresented motifs in DNA sequences, part 7 Jun 03 2008 Obtaining overrepresented motifs in DNA sequences, part 6 May 30 2008 Processing and duplicons on human chromosomes May 26 2008 That’s not a good example Kaká … May 23 2008 How British … May 21 2008 Obtaining overrepresented motifs in DNA sequences, part 5 May 21 2008 Obtaining overrepresented motifs in DNA sequences, part 4 May 12 2008 Obtaining overrepresented motifs in DNA sequences, part 3 May 12 2008 A new religion? May 12 2008 Obtaining overrepresented motifs in DNA sequences, part 2 May 10 2008 From the Interwebs “forgotten” archives … May 10 2008 Obtaining overrepresented motifs in DNA sequences, part 1 May 09 2008 Still on merging Pfam alignments … May 05 2008 Revisting Pfam alignments, again … May 03 2008 Revisiting Pfam alignments: using defaultdicts, chains … May 02 2008 Habs Apr 29 2008 Twitter Updates for 2008-04-26 Apr 26 2008 Twitter Updates for 2008-04-25 Apr 25 2008 Twitter Updates for 2008-04-24 Apr 24 2008 Twitter Updates for 2008-04-23 Apr 23 2008 How to improve scientific software? Apr 23 2008 Twitter Updates for 2008-04-22 Apr 22 2008 Twitter Updates for 2008-04-21 Apr 21 2008 XKCD got it wrong Apr 21 2008 jModelTest Apr 21 2008 Twitter Updates for 2008-04-20 Apr 20 2008 Twitter Updates for 2008-04-19 Apr 19 2008 Twitter Updates for 2008-04-18 Apr 18 2008 Twitter Updates for 2008-04-17 Apr 17 2008 Twitter Updates for 2008-04-16 Apr 16 2008 Twitter Updates for 2008-04-15 Apr 15 2008 multiGUI (restricted) beta release Apr 15 2008 multiGUI Apr 15 2008 Twitter Updates for 2008-04-14 Apr 14 2008 Twitter Apr 14 2008 Python and AppEngine in Vista Apr 14 2008 Twitter Updates for 2008-04-13 Apr 13 2008 Merging sequences from a Pfam alignment: using sets, part II Mar 30 2008 Earth hour Mar 29 2008 Merging sequences from a Pfam alignment: using sets Mar 28 2008 Awk and sed, Sed and awk Mar 28 2008 Ride to Conquer Cancer Mar 26 2008 Sad, sad day Mar 18 2008 Python sets, intersections, reduce and more Mar 17 2008 How realistic is 10,000 BC? Mar 17 2008 Python sets and intersections Mar 14 2008 GenBank parsing: both scripts Mar 14 2008 We salute you … Mar 14 2008 Fasta module: transcribing DNA Mar 11 2008 Year of the Frog Mar 11 2008 Fasta module: generating reverse complement of DNA sequences Mar 11 2008 GenBank parsing: part II Mar 11 2008 Are we there yet? Pretty much. Mar 10 2008 Parsing GenBank: getting DNA from genome entries, part I Mar 06 2008 How much would you pay? Mar 04 2008 The Sun will shine on Python Mar 03 2008 Best and worst Mar 03 2008 Burst, baby burst Feb 21 2008 A comparison between Python and C(++): parsing a GenBank file Feb 20 2008 Empires Feb 19 2008 BOSC 2008 Feb 18 2008 For every “problem” there is a “solution”. Thankfully. Feb 15 2008 Parsing a GenBank file, another approach Feb 15 2008 3 masterpieces Feb 14 2008 We are doomed! Feb 07 2008 TNT: review of the graphical interface Feb 03 2008 Is this the year Chelios retires? Feb 02 2008 Powerpoint tips Feb 01 2008 Talking about chocolate … Feb 01 2008 That’s why we pay to access scientific journals? Feb 01 2008 Ummm, chocolate Feb 01 2008 Internet Explorer 7? Are you sure? Jan 31 2008 We salute you … Jan 31 2008 Things you can only learn from Science (the journal, not science itself) Jan 30 2008 TNT: a(n) (almost) comprehensive review Jan 30 2008 Benchmarking Python: fastest way to generate unique lists Jan 30 2008 Uniquifying lists with sets and dictionaries Jan 29 2008 Python sets Jan 28 2008 A leopard almost ate my iMac Jan 19 2008 Impressive, but how do you call it? Jan 15 2008 Preaching Jan 08 2008 2007 A bit of TNT in your morning coffee Dec 19 2007 Spam Dec 05 2007 If you live in a cave Dec 05 2007 Bio::Blogs #17 - The one Santa brought us Dec 01 2007 CLC products: who uses them? Nov 30 2007 Wow! Nov 28 2007 Geneious and “specialized” software, featuring Dendroscope Nov 28 2007 Bio::Blogs #17 - call for submissions Nov 27 2007 “Cutting” chromosomes with Python: a fast approach, take two, including precision Nov 26 2007 What happened? Nov 22 2007 “Cutting” chromosomes with Python: a fast approach, take one Nov 20 2007 SciView, part 6: interview with Dr Roderic Page Nov 19 2007 Goodbye John Nov 06 2007 Can you point your country on a map? Nov 02 2007 Functional programming in Python: using filter, take one Nov 01 2007 Functional programming in Python: using map Oct 31 2007 New SciView interview coming. Oct 30 2007 Python on OSX Leopard Oct 30 2007 Merging single (or multiple) sequence FASTA files Oct 29 2007 Splitting a FASTA file using awk (no sed required), or do we care about csplit? Oct 29 2007 Generating multiple sets of random DNA sequences with one script (and a bash example) [updated] Oct 26 2007 Nobel Oct 26 2007 So, he is gone Oct 25 2007 Using subversion and svn-time-lapse to edit a manuscript, take 2, a short tutorial - PART I Oct 24 2007 Rowling: ‘Dumbledore Is Gay’ Oct 23 2007 Never trust Oct 23 2007 Using subversion and svn-time-lapse to edit a manuscript, take 1 Oct 20 2007 Watson, yet again Oct 18 2007 Off topic Oct 18 2007 Splitting a FASTA file Oct 17 2007 Watson Oct 17 2007 Alternative methods to split a FASTA file - updated (again) Oct 10 2007 Splitting multiple FASTA file, or why shouldn’t we reinvent the wheel? Oct 10 2007 Splitting a multiple sequence FASTA file, making it better Oct 09 2007 Splitting a multiple sequence FASTA file Oct 09 2007 On computer viruses and viruses Oct 05 2007 GenBank: parsing some features (and a change for the future) Oct 03 2007 Running Vista Oct 02 2007 I cringe Oct 02 2007 On “punching the liver” quotes Sep 28 2007 Hockey Sep 28 2007 GenBank files: take two Sep 28 2007 GenBank files: take one Sep 27 2007 Apart from Python and Perl in Bioinformatics Sep 16 2007 Simplicity sometimes works Sep 14 2007 Restriction enzymes: the grand finale Sep 13 2007 Restriction enzymes, third take Sep 13 2007 “bioinformatic perl or python” Sep 12 2007 CLC free workbench, a new (short) review Sep 12 2007 Ratings Sep 12 2007 Restriction enzymes: second take Sep 07 2007 Planning Sep 07 2007 Creationism and third world Sep 07 2007 Scaring Sep 06 2007 Not a very good start … Sep 06 2007 Restriction enzymes: first take Aug 31 2007 Finding motifs: IUPAC and RegEx, an approach Aug 28 2007 SciView in PDF Aug 16 2007 Thanks Tony! Aug 11 2007 SciView part 5: interview with Alexei Drummond Aug 11 2007 SciView: part 4, interview with Rosie Redfield Jul 26 2007 Call for collaboration: an Open Science (?) first for me Jul 26 2007 Finding motifs: IUPAC and RegEx, an overview Jul 16 2007 Translating DNA into proteins: second approach, now using FASTA files Jul 11 2007 Formatting output of FASTA files Jul 10 2007 Reading FASTA files Jul 04 2007 Reading FASTA files: introduction Jul 03 2007 SciView part 3: Interview with Jeremy Squire Jun 25 2007 SciView: scientific interviews, part 2 May 29 2007 Translating DNA into proteins May 24 2007 New review: CLC Workbench, free edition, and more Apr 30 2007 Genetic code: part I Apr 19 2007 SciView: scientific interviews, part 1 Apr 19 2007 Still simulation Apr 10 2007 The current state of bioinformatics software Apr 04 2007 A script to simulate DNA sequence sets Apr 04 2007 Random sequences in Python Apr 02 2007 Ramdomization Mar 30 2007 Command line arguments and a second take on functions Mar 26 2007 Python functions: simple example Mar 22 2007 Recommended read Mar 16 2007 On notes to a young computational biologist Mar 16 2007 Bioinformatics and interfaces Mar 15 2007 Debugging in Python Mar 15 2007 Section 2: a nice summary script Mar 14 2007 Writing to files Mar 13 2007 Manipulating strings: again Mar 13 2007 Wikipedia II Mar 02 2007 Beginning Python for Bioinformatics Mar 02 2007 Global warming: no memo, no report Mar 02 2007 Wikipedia Mar 02 2007 Sad news Mar 02 2007 biOpen: a review Mar 02 2007 Global warming: here to stay Mar 02 2007 Geneious: a reply from Biomatters Mar 02 2007 Geneious: one year (or almost) later Mar 02 2007 First post: a take on Geneious Feb 26 2007 Counting nucleotides: part II Feb 22 2007 Counting nucleotides Feb 22 2007 Commenting in Python Feb 22 2007 Finding motifs in DNA sequences: twist Feb 20 2007 Finding motifs in DNA sequences Feb 14 2007 Flow control in Python Feb 13 2007 “Manipulating” Python lists II Feb 12 2007 “Manipulating” Python lists I Feb 09 2007 Reading files in Python: using lists Feb 07 2007 Reading files in Python Jan 30 2007 Transcribing: the “other” way Jan 23 2007 The Regular Expression Jan 16 2007 Python printing statement Jan 15 2007 Importing and regular expressions Jan 15 2007 2006 Sequences and Strings - part II Dec 14 2006 Hands on code: Sequences and strings - part I Dec 13 2006 Why Python and not Perl? Dec 13 2006 Beginning the begin Dec 13 2006
Generating multiple sets of random DNA sequences with one script (and a bash example) [updated] Oct 26 2007
Using subversion and svn-time-lapse to edit a manuscript, take 2, a short tutorial - PART I Oct 24 2007