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darked @darked

bioinformatics/Linux NGS, Slurm, AWS, Singularity views are my own openwetware.org/wiki/User:Dare… Barcelona, Spain Joined May 2008
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Ubunta Profile Picture

ABC @Ubunta

2 years ago

Modern Data Technology Stacks for 90% of Use Cases with Minimal Costs (Non Streaming): 1. Localstack + Blob Storage + @DataPolars + Iceberg + Metabase A cost-effective setup for most use cases. Localstack emulates cloud services, Blob Storage handles data storage, Polars is used for data processing, Iceberg acts as the database, and Metabase provides visualization and advanced data modeling. 2. Localstack + Blob Storage + @duckdb + Iceberg + @metabase An alternative to Polars, DuckDB offers SQL-based analytics on local or cloud data. Iceberg and Metabase remain as the database and visualization tools, respectively. 3. @Minio + Blob Storage + Delta Lake + Polars/DuckDB + Superset Ideal for setups requiring robust UI and API integration. MinIO provides an alternative blob storage with a user-friendly interface, Delta Lake offers transactional capabilities, Polars or DuckDB handles data queries, and Superset ensures seamless dashboarding. 4. Scalable Blob Storage + Iceberg/Delta + Daft DataFrame + Metabase/Superset Suitable for scaling operations, this stack leverages Iceberg or Delta Lake for the database, Daft DataFrame for distributed data pipelines, and Metabase or Superset for dashboards. 5. High-Performance @duckdb Instance + Iceberg + Polars + Metabase Optimized for large-scale, analytical workloads. DuckDB and Iceberg manage the database layer, Polars processes the data efficiently, and Metabase offers advanced visualization.

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Ming "Tommy" Tang @tangming2005

3 years ago

Bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants buff.ly/4bviuBB

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EGAarchive Profile Picture

EGA archive @EGAarchive

3 years ago

We are happy to announce that the first #FederatedEGA dataset is now live on our website, published by the Polish Node Have a look here 👉 ega-archive.org/datasets/EGAD5…

darked Profile Picture

darked @darked

3 years ago

@mr_le_fox @duckdb @kiwipycon @Mause_me @Thijsbruineman @szarnyasg @hopsworks @SirOibaf @motherduck @tdoehmen @PyDataamsterdam @PyData Perfect. Many thanks

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DuckDB @duckdb

3 years ago

@kiwipycon @Mause_me @Thijsbruineman @szarnyasg At 15:20, @hopsworks' Fabio Buso (@SirOibaf) and @motherduck's Till Döhmen (@tdoehmen) will give a talk at @pydataamsterdam titled "MLOps on the fly: Optimizing a feature store with DuckDB and ArrowFlight". amsterdam2023.pydata.org/cfp/talk/L3WFC…

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darked @darked

3 years ago

@duckdb @kiwipycon @Mause_me @Thijsbruineman @szarnyasg @hopsworks @SirOibaf @motherduck @tdoehmen @pydataamsterdam Any chance the talk will be recorded and made accessible sometime later?

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powturbo Profile Picture

powturbo @powturbo

3 years ago

🗜️Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp 📃onlinelibrary.wiley.com/doi/full/10.10… 📀github.com/OpenGene/fastp #⃣ #DataCompression #Fastq #Bioinformatics

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Anthony Mathelier @AMathelier

3 years ago

We're excited to share our manuscript describing COBIND, a novel tool for the identification of transcription factor co-binding patterns with non-negative matrix factorization biorxiv.org/content/10.110… 1/9

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Dr Urska Demsar @udemsar

3 years ago

@KhoaVuUmn @RolandKays FYI, your video is by Jonna Jinton, a Swedish artist who lives in the Arctic and blogs about life there (this video of course a parody). youtube.com/@jonnajinton

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George Monbiot @GeorgeMonbiot

4 years ago

How do we revive our devastated planet? We don't need to speculate, as one nation has already done it. So what's stopping us? theguardian.com/commentisfree/…

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Francisco Câmara Ferreira @FranciscoCmar10

4 years ago

Four-Day Workweeks Make People Happier, More Productive, Study Shows - Blue Zones shar.es/afDujs

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SciPyTip Profile Picture

Scientific Python @SciPyTip

4 years ago

“lambda has the benefit of making the code compact and foreboding. Plus, it prevents people from trying to add meaningful names, documentation or type-hints to the thing that is about to unfold.” — @dabeaz github.com/dabeaz/blog/bl…

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Data Science Fact @DataSciFact

4 years ago

Don’t do the Wilcoxon statmodeling.stat.columbia.edu/2015/07/13/don…

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darked @darked

4 years ago

@IMIM_research @joaquinarribas @Vanesa_Nogales @hospitaldelmar @salutcat @the_prbb @UPFBarcelona @UPFbiomed @TCeliaTerrassa @BigSpinLab Correct URL: imim.cat/agenda/765/cur…

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Iwan Aucamp @aucampia

4 years ago

RDFLib 6.3.0 has been released and published to PyPI. This is a minor release with fixes and new features. For more information, see github.com/RDFLib/rdflib/… #RDF #SPARQL #Python #RDFLib #SemanticWeb

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darked @darked

4 years ago

@WEHI_research Looks like DuckDB and parquet are making inroads in bioinformatics.

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mirimiam Profile Picture

Manuel Irimia @mirimiam

4 years ago

Happy to share the peer-reviewed version of our pre-print with the @GuigoLab at @PLOSBiology ! @CRGenomica Day-night and seasonal variation of human gene expression across tissues using GTEx data. journals.plos.org/plosbiology/ar…

mirimiam Profile Picture

Manuel Irimia @mirimiam

6 years ago

Pre-print from a close collaboration with @GuigoLab: Day-night and seasonal variation of human gene expression across tissues. Leveraging the static GTEx data to understand dynamic rhythms. By Val Wucher @Reza_sodaei @RazielAmadorR @CRGenomica biorxiv.org/content/10.110…. Thread👇1/8

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darked @darked

4 years ago

@razoralign repo for the curious: github.com/samhorsfield96…

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gau Profile Picture

Maxime U Garcia | @[email protected] @gau

4 years ago

Hi @iscbsc, I remember when I was a younger researcher, working with @JeBiF into adding (or translating) @Wikipedia -> @Wikipedia_fr articles to expand global knowledge in #Bioinformatics. I just notice that both #snakemake and @nextflowio have been removed...

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darked @darked

4 years ago

@gau Same thing (neither snakemake nor Nextflow) are listed in: en.wikipedia.org/wiki/Bioinform…

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