Since each configuration file may contain conflicting settings, they are applied in the following order (from lowest to highest priority):

Parameters are applied in the following order (from lowest to highest priority):

Claude-3.5-Sonnet demonstrates excessive caution

Doesn't delete files from the destination. If you want to also delete files from destination, to make it match source, use the sync command instead.

researchers don’t consider AI today to be especially useful in guiding the scientific process,

have access to a vast corpus of high-quality open-access papers

Owl looks for previous work in a given subject area

Eric Schmidt

reprogramming endogenous proteins rather than relying on the integration of foreign DNA

order-of-magnitude acceleration of high-resolution structure prediction

if all you had done was divert money from another charity about which another equally motivated fundraiser was equally passionate.

lawyers

If the only way to make gains in the stock market was for someone else to take a loss, then the stock market wouldn't be able to go up.

Over time, trading gains outweigh trading losses for investors as a group.

I have included some of the most popular test conditions in the table below:

feel more intuitive, powerful, and cohesive thanks to its heavily customized take on GNOME, adding custom tools and extensions. It's also one of the first distros to offer NVIDIA drivers out of the box, making it a hassle-free option for NVIDIA GPU owners—such as myself.

perturbation-invariant diversity measures remain unaffected by PCR bias

While these genes would be classified as paralogs within individual genomes [32], at the population level they may be more accurately described as metaparalogs

Due to higher relative abundances of viruses on skin in some cohorts of IEIs,1616.Tirosh, O. ∙ Conlan, S. ∙ Deming, C. ..., NISC, Comparative, Sequencing ProgramExpanded skin virome in DOCK8-deficient patientsNat. Med. 2018; 24:1815-1821CrossrefScopus (101)PubMedGoogle Scholar,1717.Blaustein, R.A. ∙ Shen, Z. ∙ Kashaf, S.S., NISC Comparative Sequencing Program ...Expanded microbiome niches of RAG-deficient patientsCell Rep. Med. 2023; 4, 101205Full TextFull Text (PDF)Scopus (4)Google Scholar we also included targeted 16S rRNA gene amplicon sequencing (n = 534 samples) to analyze bacterial communities due to the risk of recurrent bacterial infections

in a series that are expected to have similar communities (i.e. longitudinal time series or cross-sectional studies where a significant portion of the strains are shared across samples

Nextflow options use a single dash prefix, e.g. -resume

In our case, we didn't explicitly mark anything else as an output, so there's nothing else there.

In our case, we didn't explicitly mark anything else as an output, so there's nothing else there.

functional dark matter

On the other hand, the dark matter in microbiology describes microbes that are right in front of us. We can lyse them, we can see them under our microscopes, we can get pieces of their genomes sequenced, and we can occasionally cultivate them.

distant proteins with essentially no sequence homology may share the same catalytic residues

This approach can also be reversed to identify novel protein functions based on unusual catalytic residues.

hinting at a potential evolutionary trajectory

(Cormode, 2011).

algorithms are allowed a single or small number of passes over the data; an excellent tutorial-style overview is by Muthukrishnan (2003) .

The ext directive can be set in the process definition:

consider an alignment-based approach like Hostile.

A good model is one that1. You understand

might delay plasmid evolution

It is currently aimed at the analysis of metagenomes sequenced using Illumina short read technology.

‘SingleM’, which estimates community composition using conserved regions within universal marker genes.

meta, fastq ->

When a process is invoked in a workflow, it must be provided a channel for each channel in the process input section

SYNBIO AUCTIONHANDBOOK22.4.19Made with ❤ for D.A.V. Public School, VelacheryiGEM 2019 SASTRA Team - Human Practices #1

NSM is more accurate than mechanistic or machine learning components on experimental datasets

During the next 25 years, hundreds of scholarly articles cited the letter—in many cases overgeneralizing or omitting key details, potentially helping drive overprescription of opioids in the 1990s and contributing to the ensuing wave of overdose deaths, a 2017 analysis found.

I will not be arrested and deported for writing this essay. In that respect, the legal value of my citizenship remains secure. But what that citizenship is worth, on a deeper level, feels imperiled.

nextflow pull nf-core/demo Nextflow will pull the pipeline code, meaning it will download the full repository to your local drive.

Many binning methods have been developed

amplified

“PacBio CCS” datapoint was taken from a 2019 publication that does not represent today’s performance. For example, Karst et al. (2021) described HiFi sequencing of full-length (4.4 kb) rDNA amplicons of the same sample at 99.9993% (Q51.5) accuracy, almost two orders of magnitude greater than the previous study.

We would like to thank E. Simon and J. Silberg for their helpful discussions of this work.

requires reasoning across diverse fields from biology to computer science

Virtual Lab consists of an LLM principal investigator agent guiding a team of LLM agents with different scientific backgrounds

shows that the internal organization of concepts in the AI model corresponds, at least somewhat, to our human notions of similarity.

measure a kind of "distance" between features based on which neurons appeared in their activation patterns

nouns in mathematics

All non-mandatory command-line tool non-file arguments MUST be provided as a string via the $task.ext.args variable.

Flexibility: Users can easily customize module behavior without modifying the module code itself
Separation of concerns: Module logic stays separate from parameter configuration
Reusability: The same module can be used with different parameters across different pipelines
Consistency: All nf-core modules follow the same pattern for optional arguments

Input channels: Mandatory non-file arguments that are essential for the tool to function (e.g., required modes, essential parameters)
ext.args: Optional flags, parameters with defaults, or any non-essential command-line options

Web application that comprehensively determines the composition of a shotgun sequence data set. It should take about 10 seconds to process an uploaded sample.

If you want a full taxonomic breakdown of your sample

anytime a justice writes separately, the question is always why: Who is it for, and what does the justice hope to accomplish by voluntarily doing extra work?

A central bank able to control domestic interest rates is a sufficient condition to allow a government to freely pursue countercyclical fiscal policy with no danger of a runaway increase in the debt ratio.

valuable knowledge across diverse microbial species

microbial pangenomic research

[17].

Thankfully, the development of AI technologies, especially Large Language Models (LLMs) [8, 9, 10] with strong reasoning, adequate knowledge reserve and excellent coding capabilities [11], is reshaping the paradigms and precepts of how people leverage bioinformatics data.

Domain specialization as the key to make large language models disruptive

emergence of large language models presents an opportunity to speed up the text-mining of protein activities for biocuration

Provided the manuscript, FuncFetch extracted data such as species information, enzyme names, sequence identifiers, substrates, and products, which were subjected to extensive quality analyses

precision/recall of 0.86/0.64 in extracting substrates

identified multiple extraction errors including incorrect associations, nontarget enzymes, and hallucinations, which highlight the need for further manual curation

Performing these tasks requires the installation, integration, and tuning of multiple software packages, which is not trivial even for groups with extensive bioinformatics expertise. As a result, most studies rely on ad hoc pipelines based on custom scripts and intensive manual analyses, making it difficult to reproduce or extend analysis results and hampering collaboration.

that the choice of assembler has a strong influence on the final assembly results and choosing the ideal assembler requires taking into account both contiguity and correctness

explained in part by the library size re-estimation automatically performed within the MetAMOS preprocessing stage

level of improvement provided by MetAMOS over other assembly tools is highly dependent on the specific characteristics of the dataset being assembled

aggressive assembly approaches sometimes result in more contiguous assemblies, but often introduce errors of the most severe kind (chimeras)

it can be difficult to choose an appropriate assembler a priori

motivates our focus on fast end-to-end analysis and inclusion of multiple assembly methods, allowing the user to tailor the pipeline to their data

MetAMOS makes it straightforward to assess the performance of the various tools for each of these steps for a given sample.

this framework will reduce duplication of efforts

allowing scientists to focus their attention on individual components without having to re-implement all the components of a metagenomic pipeline

At the end of the final stage, MetAMOS produces an interactive HTML report that summarizes the main results of the run

the entire pipeline is built around the unique features provided by the metagenomic scaffolder Bambus 2

the installation, integration, and tuning of multiple software packages, which is not trivial even for groups with extensive bioinformatics expertise.

tools tied together with the help of the lightweight workflow system Ruffus

MetAMOS can be viewed as an assembly-centric counterpart to QIIME

push-button solution for analysis of metagenomic datasets

most studies rely on ad hoc pipelines based on custom scripts and intensive manual analyses, making it difficult to reproduce or extend analysis results and hampering collaboration

MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations

the advantages of computational pipelines over ad hoc scripts, even for simple tasks, are all more apparent with increasingly complex datasets and the use of parallel processing.

the advantages of computational pipelines over ad hoc scripts, even for simple tasks, are all more apparent with increasingly complex datasets and the use of parallel processing.

‘Make’ specifications are written in an obscure and limited language

Automatic data tracking in pipelines allows only the out-of-date parts of the analyses to be rescheduled and recalculated, with minimal redundancy

same ‘rule’ can be applied to multiple data files at the same time

‘make’ has been widely used to keep track of dependencies in scientific pipelines

In contrast to Pwrake and GXP Make, Snakemake does not rely on any password-less SSH setup or custom server processes running on the cluster nodes

Snakemake is the first system to support file name inference with multiple named wildcards in rules

By default, Snakemake only executes rules if the output files are not present or the modification time of the input files is newer

automatic deletion of output files from incomplete rule executions (e.g. due to a failing shell command)

Despite the short history of bioinformatics, several software efforts have evolved into a pipeline model

development of sequence assembly tools and genome annotation systems

running analysis in a serial rule-dependent fashion (workflow) and (2) the ability to run these tasks in parallel where possible (high-throughput).

Protocols also make for easy benchmarks

encourage software reuse by providing modular components

connecting different software applications together, file format conversions

“scripting glue,”

designed to work over a compute farm

easier for experimentation and replication

need for introducing an explicit protocol-based approach to bioinformatics analysis that will lend rigorousness to the analysis

bioinformatics framework must be flexible and generic enough to accommodate such changes

federation of databases

bioinformatics analysis to be carried out in a paralle

A clear statement of the nature of the intrusive judicial inquiry a parent company could be subjected to in such cases was provided by Lord Bingham when the litigation reached the House of Lords as follows:

CD8-depletion antibodies

When I began my work, jazz was a stunt,” was Duke Ellington’s later critique of some of this music11Close—but the slick professionalism of the Harlem stride style also served to expand the audience for African American music in the face of discrimination from cultural elites, both within and without the black community, and despite a severe economic downturn.

within the internal perspective. They are first-order claims about what is right or wrong in specific counterfactual conditions, and can thus be glossed in expressivist terms. This is underpinned by the fact that our moral attitudes respond to natural features of the world. We judge that kicking dogs is wrong because of the pain they suffer when kicked, not because we happen to disapprove of such behaviour. Quasi-realists can therefore hold that kicking dogs remains wrong in worlds at which our counterparts approve of it, for o

Moreover, just like cognitive disinhibition, schizotypy is correlated with creativity, verbal and visual, with one caveat: Desiring isolation, being introvertive, lacking a capacity for pleasure—these do not predict creativity. They don’t make you more creative, according to the studies.

hey made themselves schizotypal

that he purposefully overrode,

with no regard for the truth of the assertion. To others and to himself, he willfully defied reality. He’d reverse himself, too. If particular lines of argument failed to persuade, he’d advocate others. He’d throw people off by adopting their position as his own. He’d say an idea was crazy, then a week later call it great.

And since you can’t connect what never gets in, art is enhanced potential for connectivity.

Run a generative AI chatbot on Jetson Orin Nano Super Developer Kit. This chatbot features Ollama with Open WebUI, a widely used, open-source, chatbot server interface that connects to locally running LLMs.

npm is a couple of things. First and foremost, it is an online repository for the publishing of open-source Node.js projects. Second, it is a CLI tool that aids you install those packages and manage their versions and dependencies.

our model solves 28.8% of the problems, while GPT-3 solves 0% and GPT-J solves 11.4%

translates whole-programs from one high-level programming language to another

symbolicexecution (symexec)

theoretical framework is needed to represent the complex interactions that drive these dynamics

successful establishment of the organism into the community

Omi: Bridging the Bioinformatics Expertise Gap with a Natural Language-Driven Metagenomics Co-pilot

Domain specification techniques are key to make large language models disruptive in many applications

many hurdles, caused by the heterogeneity of domain data, the sophistication of domain knowledge, the uniqueness of domain objectives, and the diversity of the constraints

we present a comprehensive survey on domain specification techniques for large language models, an emerging direction critical for large language model applications

LLMs, significantly outperforming smaller models in understanding and generating human-like text,have emerged as a promising AI research trend

efficient literature analysis, novel hypothesis generation, and complex data interpretation

domainspecialization of Large Language Models (LLMs) is defined as the process of customizing general-purpose LLMs accordingto specific domain contextual data, augmented by domain-specific knowledge, optimized by the domain’s objective, andregulated by domain-specific constraints

Parameter-efficient fine-tuning (PEFT)

additive adapters applied to frozen model weights

suboptimal model quality due to restrictive assumptions

sketching, a popular data compression technique, can serve as an efficient adaptation strategy for LLMs while avoiding low-rank assumptions

compresses LLM weights into compact fine-tunable sketches

faster and more memory-efficient training and inference

evaluations with Llama-1/2/3 models

diverse tasks including math problem-solving, common sense reasoning, and instruction following

labor-intensive workflows

SpatialAgent, a fully autonomous AI agent

SpatialAgent integrates large language models with dynamic tool execution and adaptive reasoning

combining autonomy with human collaboration

complex high dimensional data

computational methods that are quite fragmented

extensive human intervention

users have to reason over multiple analysis approaches

require deep biological knowledge

from experimental design to multimodal analysis and data-driven hypothesis generation

predefined workflows and rigid models, SpatialAgent employs adaptive reasoning and dynamic tool integration, allowing it to adjust to new datasets, tissue types, and biological questions

supports human-in-the-loop interactions

tasks such as gene panel design, cell and tissue annotation, and pattern inference in cell-cell communication and pathway analysis

Key modules. The action module (left) executes tasks such as retrieving reference datasets, converting gene names, verifying ligand–receptor interactions using existing databases, processing data with established software packages (e.g., numpy) or generating and executing custom code, while reasoning over and aggregating information from multiple sources

SpatialAgent consists of three key modules (Fig. 1b): memory, planning, and action.

Wratten, L., Wilm, A. & Göke, J. Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nat Methods 1–8 (2021) doi:10.1038/s41592-021-01254-9.

barrier is overcome by workflows, which implement popular analysis strategies

accessible to those who have limited training in computation

the ability to analyse data beyond predefined strategies they implement continues to be largely limited to ‘master chefs’

microbiologists who wanted more freedom in research questions they could ask of their data

interactive refinement

interactive visualisation and editing software

more than 100 interoperable programmes

Nano (8B)

open family of heterogeneous reasoning models that deliver exceptional reasoning capabilities, inference efficiency, and an open license for enterprise use.

performs competitively with state-of-the-art reasoning models such as DeepSeek-R1 while offering superior inference throughput and memory efficiency

using neural architecture search from Llama 3 models for accelerated inference, knowledge distillation, and continued pretraining, followed by a reasoning-focused post-training stage

support a dynamic reasoning toggle, allowing users to switch between standard chat and reasoning modes during inference

early tools such as NPLinker190, GraphOmics200 and anvi’o201 are starting to overcome some of these challenges

Another bottleneck is getting the data in the appropriate format so it can be used by AI algorithms

anvi’o75 was used to profile and visualize the different Turicibacter strain DNA sequences to locate putative bile salt hydrolase and 7α-HSDH homologs in contig groups, generate variability profiles, and measure gene coverage and detection statistics.

Yet, taxonomic insights offer limited utility to understand functional drivers of biological systems, a pinnacle desire that brings together many corners of microbiology

Understanding of microbes in their environmental context required genomes

ability to reconstruct microbial genomes directly from the environment

can provide clues regarding metabolic requirements of little-known organisms and guide their directed isolation

careful interpretations of variants observed in metagenomes are becoming more accessible through integrative ‘omics platforms223

computational resources and large datasets required, however, limit their applicability in biological contexts

scaling up foundation and task-specific models

introduce Lyra, a subquadratic architecture for sequence modeling, grounded in the biological framework of epistasis for understanding sequence-to-function relationships

plasmid binning, that is identifying plasmids in sequenced bacterial isolates

we propose the use of a pangenome graph, built from assembly graphs produced by assembling short reads of the same sample with different assemblers

highlights similarities between contigs from different assemblies while retaining information on contigs that appear only in one of the input assemblies

Constructing a pangenome graph, however, is still a time-consuming and expensive process.

augment a pangenome graph using unassembled reads

does not require to align them and genotype the new individuals

present the first assembly-free and mapping-free approach for augmenting an existing pangenome graph using unassembled long reads from an individual not already present in the pangenome.

agentic technology uses tool calling on the backend to obtain up-to-date information, optimize workflows and create subtasks autonomously to achieve complex goals.

autonomous agent learns to adapt to user expectations over time.

ability to store past interactions in memory and plan future actions encourages a personalized experience and comprehensive responses

agent can update its knowledge base and perform agentic reasoning

each step of the way, the agent reassesses its plan of action and self-corrects, allowing for informed decision-making.