WHERE TRUE Technologies
@WHERE_TRUE_TECH
Followers
33
Following
1
Media
23
Statuses
47
We've released initially support for SDF files in biobear and exon. Learn more here: https://t.co/9fYx5p61jO.
0
1
0
Notes on our latest release: https://t.co/C5clvCh7jY... it's now possible to `COPY` from tables into FASTA or FASTQ files. You can also go straight to integer encodings for DNA and AAs from FASTA files for faster training and inference.
0
0
2
If you're more interested in how to get setup for a pLM from raw sequencing data, you can start here:
0
0
0
New video where we look at what a join is in SQL, then the see how to join together a sequence dataset, extract CDSs and AAs, then run them through Group K-Fold cross validation to get set-up to train a pLM for back-translation
1
0
3
Want to upload VCF data to your data warehouse with queryable structs for the complex fields like INFOS? See this short tutorial to learn more:
0
0
2
New version of biobear was just released with lots of improvements. Here we see: - More pythonic API, especially for DataFrame use - Type annotations for API discoverability in your editor - CRAM file support
0
0
2
See the updated docs here:
wheretrue.dev
Exon brings database concepts to scientific computing in order to improve the management and processing of data.
0
0
0
A couple of updates to our documentation... 1) we have an expanded Nextflow example showing Exon's use with Prodigal for cataloging annotation output. 2) we're now shipping binaries for commonly used platforms, so our CLI page is updated to show how to get them.
1
0
0
BioBear hit 100 stars on GitHub recently. Thanks to everyone for your support!
github.com
Work with bioinformatic files using Arrow, Polars, and/or DuckDB - wheretrue/biobear
0
2
3
Already using Nextflow? See how you can easily extend your pipelines to support your data engineering needs without a separate system.
wheretrue.dev
We've begun publishing the Exon CLI to the AWS Public ECR. This means you can pull and run the Exon CLI using Docker, and use it interactively or in scripts and workflows, like Nextflow which we'll...
0
1
2
New exon release includes table functions, indexed GFF file, FCS file, and other improvements. Check out the post here for more info: https://t.co/jNHWl5pE21
0
1
0
Interested in using Delta Lake for your bioinformatic data? See how BioBear can help.
wheretrue.dev
A goal of BioBear and WTT writ large is to bring bioinformatics data handling into the Data Lake era. "Data silos" is a bit trite, but it's true that bioinformatics data is often stored in a variety...
0
1
1
We've release initial support for the postgres wire protocol to Exome. This means you can use common postgres tools to connect directly with your bioinformatics data. See our blog post for more, including temporary limitations (no pg_catalog support). https://t.co/ftLAExHB9r
0
0
0
New feature just shipped in Exon: hive partitioning for bioinformatic files. Read about it, new ExonR SQL Sessions, and GitHub Sponsor activation.
wheretrue.dev
In addition to launching the public preview of Exome last week, we've also made some updates to Exon.
0
0
2
Exome, our OLAP warehouse for biotech & life sciences is open for technical preview. Please give it a shot and let us know what you think! https://t.co/1EFw1SVaC3
1
2
3
We've updated our website to reflect the tools we've made available or are in the process of 😼: https://t.co/guFhNjcLpw -- please give it a look
0
0
0
Sharing few recently shipped updates: 1. BioBear now exposes a SQL session, making it easier to use in ETL and local use-cases. 2. Exon support projection and predicate pushdowns for BAM files. See post for an example of 14GB 10x Genomics Dataset. BioBear session for ETL:
1
0
0
We've released Exon 0.3.0, and with it came significant performance improvements to the VCF component while keeping an interface that is germane to SQL. @trent_hauck wrote about it here:
0
0
1