dalke

56 ms·

1. 421.▲
   The chemfp project: problems selling free software(jcheminf.biomedcentral.com)

   1 points by dalke 6y ago|3 comments
2. 422.▲
   by dalke 6y ago

   Where is gen220 rewriting Python history? Rust is a pretty obscure language now in pretty much the same way that Python was an obscure language then . Of course the world of programmers was smaller in the 1990s. But if your baseline is t
3. 423.▲
   by dalke 6y ago

   Python's first posting to Usenet (v 0.9) was in 1991. The 1.0 Misc/ACKS from 1994 includes 50 or so external contributions to that point, showing that "1.0" is a somewhat artificial point. Rust's 1.0 was 2015, which
4. 424.▲
   by dalke 6y ago

   On 2D molecular similarity search, yes. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-0... . The general approach reduces a 2D molecular graph into a 1D bitstring "fingerprint" which is repr
5. 425.▲
   by dalke 6y ago

   While true (I make a living working with them), I don't think the OP is that interested in graphs which are that small. What makes molecular graphs a bit more challenging is that there are 1 billion or so "small" graphs to se
6. 426.▲
   by dalke 6y ago

   A molecular structure viewer/browser/search plugin for JupyterLab for SDF and SMILES files. It should work as filetype viewer and inline in the notenook. Preferably using RDKit. I've been wanting that for several years. Never
7. 427.▲
   by dalke 6y ago

   I wrote bioinformatics software a long time ago. Meaning that I remember reading the bioperl code back to read FASTA files around Y2K. Their technique is still in use, at https://github.com/bioperl/bioperl-live/blo
8. 428.▲
   by dalke 6y ago

   Even with the British spelling? ;)
9. 429.▲
   Computing in Colour (2013)(gresham.ac.uk)

   17 points by dalke 6y ago|3 comments
10. 430.▲
    by dalke 6y ago

    I heard about TileDB because one of the authors commented at https://news.ycombinator.com/item?id=22423632 . That discussion includes what you mentioned, plus a mention that it integrates with MariaDB, PrestoDB and Spark, i
11. 431.▲
    by dalke 6y ago

    Fun bit of trivia: the first two major web libraries - cgi-lib.pl and CGI.pm - were written by bioinformaticians. Steven E. Brenner and Lincoln Stein, respectively.
12. 432.▲
    by dalke 6y ago

    The highlighted new features for version 2.0 are: 1) Support for heterogeneous dimensions in sparse arrays (that is, full dataframes), 2) Support for string dimensions in sparse arrays, 3) Google Cloud Storage and Azure Blob Storage support
13. 433.▲
    TileDB 2.0 and the Future of Data Science(medium.com)

    81 points by dalke 6y ago|33 comments
14. 434.▲
    by dalke 7y ago

    I haven't consented to the WaPo site so not read the article. I live in Sweden, with preschoolers. Unlike in neighboring Norway and Denmark, the preschools and elementary schools have not closed down. According to https://ww
15. 435.▲
    by dalke 7y ago

    I'm probably the Mooers' expert here on HN. Mooers worked at the Naval Ordnance Lab headed by John Atanasoff, of Atanasoff-Berry computer fame. He was one of the very first people working on digital computers. (Eg, see https:&#x2
16. 436.▲
    by dalke 7y ago

    Thanks for confirming that. Looks like I'll need to look elsewhere for the next chemfp fingerprint file format.
17. 437.▲
    by dalke 7y ago

    Thanks Jeremy. I looked at Feature, and the underlying Arrow format, but couldn't figure out how to implement a row-id-label-to-row-index dictionary. The only "dictionary" I saw was for categorical data. I had the same issue
18. 438.▲
    by dalke 7y ago

    Given the discussion on Zarr, HDF5 and TileDB, I hope I can get feedback from a problem I have. I want to switch from a format I made (the "FPB" format described at http://chemfp.com/fpb_format/ ) to one whic
19. 439.▲
    by dalke 7y ago

    Thanks for the pointer. And praise. I have several bios out there, for different purposes. I should update that one .... and the web site. Been meaning to do that for a long time. sigh I don't have the interest to evaluate Seq. I onl
20. 440.▲
    by dalke 7y ago

    FWIW, SARVAVID is mentioned in the "Related Work" but "it lacks generality". And "Biopython" is misspelled as "BioPython." A common mistake.
21. 441.▲
    by dalke 7y ago

    Page 125:3 makes the claim "We introduce Seq, the first domain-specific language and compiler for computational biology" without further qualifier, so I think my interpretation is correct.
22. 442.▲
    by dalke 7y ago

    Thank you! I remembered a group in Europe developed a language, but I couldn't remember the name - that was it!
23. 443.▲
    by dalke 7y ago

    I did say it was 20 years ago. ;) Since then I've been working in cheminformatics. Which has its own forms of insanity.
24. 444.▲
    by dalke 7y ago

    There's a comma before that clause, which suggests that it's not meant to be interpreted as "the first bioinformatics-specific programming language to marry C and Python" but rather as "the first bioinformatics-spec
25. 445.▲
    by dalke 7y ago

    What does "first language tailored specifically to bioinformatics" mean? I ask because I'm pretty sure there have been earlier languages for bioinformatics. Just looking around I see: - "Composable languages for bioinfor
26. 446.▲
    by dalke 7y ago

    "Often a regexp can match in many ways ..." When I worked in bioinformatics, some 20 years ago, I implemented a SWISS-PROT to regex converter. I ended up having to ask SWISS-PROT was if certain patterns were meant to be greedy or
27. 447.▲
    by dalke 7y ago

    The article was pretty clear this wasn't about gender equity but about the mode of transportation. Quoting the text, " In fact, it turned out that the pertinent point was not about gender balancing specifically. The data showed t
28. 448.▲
    by dalke 7y ago

    While I don't believe it's getting worse. Objective-C dates from the 1980s, and I'm surprised you needed anything from C++ which wasn't available in the C that Objective C supports. Python doesn't encourage a sing
29. 449.▲
    by dalke 7y ago

    Taking the tangent further, you write "one of my pet peeves with today's programmers". As someone who started programming in the 1980s, I've observed both sides of the issue. When I started, the earlier generation compla
30. 450.▲
    by dalke 7y ago

    I don't understand your question. I think you're asking if APL and/or J supports a sparse matrix representation, such that the one-liner scales as expected for the Tarjan algorithm. As I wrote, I don't know more than a t