jerven

7 ms·

31.
by jerven 3y ago
Me too! it is funny having done it a few times I got used to it but I would love to get rid of it.
32.
by jerven 3y ago
> and often don't even capture the molecule pose as it would appear in biology. Mapping between ligands in PDB and cognate ligands as being annotated in UniProt is improving :) my UniProt curator colleagues are working hard on this.
33.
by jerven 4y ago
Rdf-star workgroup has just started and they will update some parts of sparql rdf etc. They are also looking at making it easier to update. I.e. living standards like.
34.
by jerven 4y ago
Graph, alone does not make a selling feature list. You need to bring more to the long term enterprise problem space. i.e. otherwise it is just one more specific database for one or two projects, with annoying sales and contract negotiations
35.
by jerven 4y ago
I like JEPs such as this one. They show a strength of the current Java platform development community. We see multiple people spending significant thoughts and effort on what looks like a small feature. Which when implemented aims to feel s
36.
by jerven 4y ago
I think you are talking about this example: ResultSet rs = DB."SELECT * FROM Person p WHERE p.last_name = \{name}"; This when it becomes valid java will not allow an SQL injection attack. The name part would be properly passed as
37.
by jerven 4y ago
Probably, but in this case. It is also a lot of where next in line after the Ukrainians. Because if Putin thinks it is worth invading Ukraine then he thinks the same of Poland. And if successful there then Germany is next, etc. The domino t
38.
by jerven 4y ago
Well the replacement of this code base uses Solr. But when legacy started we where on lucene 1x that over the years upgraded to lucene 9x. So one of the things we used our bitmaps for was for a number extensions to pure lucene. So like face
39.
by jerven 4y ago
I love roaringbitmaps and maybe even over use this library. On the other hand it made a lot of things possible for legacy.uniprot.org over the years that would have been unaffordable otherwise. Quick faceting using permanent filters over 50
40.
by jerven 4y ago
The website not the Pfam database. Considering InterPro and PFam are under the same cluser head Alex Bateman at EBI this makes sense. So this page goes away https://pfam.xfam.org/family/PF02171 while this page remains
41.
by jerven 4y ago
This is an important point, a lot of this data is practically unfindable and databases like Rhea [1] for reactions of biological interest are also barely funded. Generating and maintaining these databases is not very expensive but not sexy
42.
by jerven 5y ago
Used to, OpenJDK is licensened under GPLv2 with the classpath excemption that allows this for years. If not running an OpenJDK build it depends on your vendor license.
43.
by jerven 5y ago
I would love to see this as well. Or even plain compared to plain downloading from an FTP site. Especially for large files 10GB plus in size.
44.
by jerven 5y ago
Yes a lot. https://rust-for-linux.github.io/docs/alloc/alloc/index.html
45.
by jerven 5y ago
Even with the old data in https://susproc.jrc.ec.europa.eu/product-bureau/sites/defaul... This is getting better and better, with lower carbon footprint each new generation. With payback times as low as 4 months,
46.
by jerven 5y ago
Working with one of the team providing the uniref dataset used here. Running any kind of torrent stuff in an university network setting is a central policy fight one just does not want to get into at all. On the other hand outbound network
47.
by jerven 5y ago
I would upvote this twice if I could. Life science quite often NP-hard still approximate results are extremely useful. Joke, which I think is from Sean Eddy (hammer). Bioinformatics approaches a Computer Scientist for help with a hard probl
48.
by jerven 5y ago
For one of the sites I work with. Headless chrome defenitly inflates the GA user numbers. We can spot this because they tend to come from big cloud data centre locations when doing ip to geo mapping.
49.
by jerven 5y ago
Interesting read. I think there are some ideas in there that can be used for sparql 1.2. especially regarding external function definitions. On the other hand the sparql in the paper is decent but not excellent. The result is subtly differe
50.
by jerven 5y ago
No, https://www.kegg.jp/kegg/legal.html
51.
by jerven 5y ago
I would have a look at Rhea. Which is not a pathway database but a which chemical reactions are out there in biology. This can be combined with the data in UniProt to build metabolic pathways. And then at metanetx.org to build draft metabol
52.
by jerven 5y ago
Paperwork trickery will be harder, as they can't be subsidiaries. So it has to be a real sale to a real external company. This takes time and money and basically means getting out of the refinery business. This doesn't change anyt
53.
by jerven 5y ago
The comment is that "The Sveriges Riksbank Prize in Economic Sciences in Memory of Alfred Nobel 1974 " is not really a Nobel prize, as it was not set up by Nobel.
54.
by jerven 5y ago
I think this has always been the case no matter what language is used. Body shops push crap, it is just the way of life. It can be crap java, javascript or kotlin the fundamental of why they are shoving crap is not going to change because o
55.
by jerven 5y ago
Ask a man how many guys he has dated. What is the more common connotation? Which is why it is about men first and women second in likelihood. Not about precedence of importance but precedence of likelihood about the genders of the people sp
56.
by jerven 5y ago
No "guys" is not inclusive in many situations. Guys is males first, female second.
57.
by jerven 5y ago
All very fair points. But I think the ecosystem of a language is part of this discussion. And the ecosystem of year 2000 C++ is hard to run on current systems. While the ecosystem of year 2000 java still works.(IMHO better than 2005 java) I
58.
by jerven 5y ago
Yes, the C++ dependencies are unlikely to be available. Specifically dependencies on OS libraries that are just not available on current common systems. So you need to get them but they are not available anymore and may depend on code that
59.
by jerven 5y ago
This, so much this. The value of code just working and staying working is humongous. Having code that is unchanged from Java 1.3 doing it's thing and delivering value 21 years later without needing to be touched and revisited allows us
60.
by jerven 6y ago
Baseload tends to be about 40% of max load in most grids. i.e. having base production doesn't really change the economics of storage or over-provisioning etc. On the other hand because there is always, in this theoretical grid 60% over

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