Some initial results from the #CASP15 competition and we see that #Alphafold2 has become a fertile ground for experimentation by several research groups around the world. Facebook's ESM protein language models (pLMs) are the top non-MSA based methods.
Another slide showing some of the experimentation taking place: increase the number of models, recycles, get more diversity using dropout (how would that work?), subsample MSAs.
A slide showing the amount of #GPU hours used for computing the structures in the #CASP15 dataset.
How quickly things progress: we are now treating naive AF2-Multimer as the starting point onto which we make improvements.
Here showing some of the remaining challenges for AF2-Multimer, including Antibody & nanobody completes and Mutation-induced changes.
On the topic of folding predictions for Antibodies, we got lots of great data for SARS-CoV-2 in the last couple of years. Some example predictions on these here.
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In #NextGenerationSequencing news, we look at the clinical uptake of different NGS technologies after the recent updates announced in the last few months:
NGS has been dominated by Illumina with their SBS short-reads technology, with reads of up to 2x150 base pairs available in most configurations, although 2x300 are also possible at a higher cost per Gb.
If we could roll back time in the last 15-20 years of NGS history, we would ideally have had a long-reads technology, or better yet, a length agnostic technology, be the dominant player, as most applications, both in Life Sciences Research and Clinical, would have benefited
In Next-Generation sequencing news, we have been digesting the Chemistry X and $200/genome announcement by $ILMN Illumina for a few weeks now, and next in line are $PACB PacBio, MGI Tech and $ONT.L Oxford @nanopore to give updates between now and the year end.
The $200/genome announcement by Illumina puts pressure on the other short-read high CAPEX instrument companies, which at the moment would be MGI Tech and Ultima Genomics. Both will have to deliver on their promises of a $100/genome, which they both have made recently.
In terms of the long-read market, the $200/genome is a still a short-read play, and thus should not put pressure on PacBio and Oxford Nanopore in that regard. Illumina had to concede that long reads are important, and their Infinity technology strategy is a demonstration of the
Some back of the envelope calculations on the recent announcements by $ILMN Illumina make me think there may have been two lines of pricing being considered when launching the NovaSeq X Plus instrument line. The "conservative pricing" could have placed the 25B flowcell at $3/Gb.
Then placing the 10B flowcell somewhere in between the $3/Gb and the $6/Gb on the NovaSeq 6000 instrument, maybe at $4.5/Gb.
This would probably have matched MGI Tech's unofficial pricing of $6/Gb on the mid-throughput sequencer, where Element Bio @ElemBio is also priced.
And their DNBSEQ T7 equivalent to the NovaSeq 6000 at $4.5/Gb, maybe better? Their DNBSEQ T10x4 could already be at $1/Gb, but it's a larger installation and commitment than the NovaSeq X Plus 25B flowcell (H2 2023), and pricing isn't clear on it yet.
Another day, another tweet about Next-Generation Sequencing, this time comparing four companies that have a play in short-read NGS with markedly different histories so far: $ILMN Illumina, $OMIC Singular Genomics, Element Bio @ElemBio and @UltimaGenomics :
All four companies listed here are in the short-read Next-Generation sequencing realm, with Illumina being the 800-pound gorilla of NGS with 80-90% of the marked share, and having recently announced their NovaSeq X Plus instrument line to consolidate their leadership in the
high-throughput part of the market. Second is Ultima Genomics, which is a private company that recently came out of stealth, and announced their plans to release a high-throughput short-read sequencer in 2023 capable of doing $100 genomes ($1/Gb). No confirmation on the price
Thank you all who followed the $ILMN Illumina updates last week via this twitter account. I suspect things will calm down until the next announcement in NGS ($PACB PacBio / $ONT.L Oxford Nanopore / MGI Tech in the next few weeks). Meanwhile I'll carry on tweeting...
As well as:
Bioinformatics Compute Acceleration (bit.ly/biocompute / more on the Computers geeky side)
Biotech stocks and tech stock market trend (bit.ly/biotech-slides financial/strategic as well as the technical/scientific side)