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#methods

2 posts2 participants0 posts today
Public
Philo Sophies

#Zoomposium with Prof. Dr. #Konrad #Kording: “How do #machines think?”

The old #Atari games were run on a very simple, old #processor. The #dynamic #processes of this “very simple, #artificial #organism” were then analyzed using #neuroscientific #methods in order to obtain #information about what actually “happens” - in the truest sense of the word - in its #logic #gate #network.

More information: philosophies.de/index.php/2024

or: youtu.be/lLHg9fk3Zdw

photo of Konrad Kording
Public
UniversityofGroningenLibrary

"Publishing #diamond #OpenAccess is a noblesse oblige for us. Let everyone benefit from research, so that we contribute together to appropriate care and improve the quality of life for people with #intellectual #disabilities."

Read the interview with Alain Dekker, editor of an open access book on #psychosocial #support #methods:

🔗 rug.nl/library/open-access/blo

The book, published in 2024, has been downloaded >10,000 times by now.

#research #care #psychology #SocialWork

📷 by Silvio Zangarini

Dr Alain Dekker, Photo by Silvio Zangarini, University of Groningen Honours College
Public
Bioinfhotep

link.springer.com/article/10.1
#networksAnalysis #rstats #methods #bioinformatics

SpringerLinkCross-validation for training and testing co-occurrence network inference algorithms - BMC BioinformaticsBackground Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation. Results Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability. Conclusions Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method’s applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.
Public
svoop ✊

Here's a #Ruby #design #question that regularly pops up in various contexts such as this: The Mailjet gem is a REST API adapter, 99% generated code. It exposes things as #class #methods like `Mailjet::Contact.create`. For a simpler, more consistent interface, I'm wrapping these in my own #PORO service class, all class methods as well, but I don't like this orgy of `class << self`. How to better design this? Here's a gist with the method bodies removed for readability: gist.github.com/svoop/25accb41

GitHub Gist: instantly share code, notes, and snippets.
Gist1_webhook_service.rbGitHub Gist: instantly share code, notes, and snippets.
Public
Frédéric Rimet

and this paper also in MBMG erally nice : good work Tiina 😀
mbmg.pensoft.net/article/13083
Technology Readiness Level of biodiversity monitoring with molecular methods – where are we on the road to routine implementation?
by Laamanen et al.
#edna #methods #TRL #metabarcoding #standardisation

Metabarcoding and MetagenomicsTechnology Readiness Level of biodiversity monitoring with molecular methods – where are we on the road to routine implementation?Human activities are causing rapid biodiversity loss across ecosystems, affecting human well-being and crucial ecosystem services. Traditional biodiversity monitoring tools cannot keep up with the increasing demands of monitoring due to their limited spatial or temporal coverage, high costs, and lack of taxonomic expertise. Thus, implementation of novel molecular monitoring methods such as environmental DNA (eDNA) and DNA metabarcoding, are necessary. Molecular monitoring methods offer significant benefits for biodiversity monitoring and environmental assessment: high sensitivity and accuracy, non-invasive sampling, broad taxonomic range and cost and time efficiency. However, the diverse methodological approaches lead to poor comparability between studies and surveys, highlighting the need for standardised assessments. We used the Technology Readiness Level (TRL) framework to evaluate the maturity of molecular monitoring methods, providing a structured assessment of their readiness for routine use. In a systematic literature review, 420 articles fulfilling the study criteria were assessed and both individual studies and method categories ranked according to the TRL scale. The findings revealed a growing number of studies, particularly in aquatic environments, with most studies validating molecular technologies on a small scale but lacking large-scale system demonstrations. Aquatic eDNA-based methods targeting fish showed overall higher technology readiness compared to other sample types and taxa and applications of molecular monitoring methods ranked into the highest TRL were predominantly freshwater studies. Key barriers to the broader implementation of molecular methods to monitoring include the need for international standards, better quantitative estimates and comprehensive reference libraries. National and international cooperation is crucial for establishing common standards, ensuring reliable and comparable results and expediting the routine use of molecular methods in biodiversity monitoring. Recent efforts towards international standardisation are encouraging, but further coordinated actions are necessary for the global implementation and acceptance of these methods.
Public
Frédéric Rimet

Nice paper in MBMG about eDNA methods standardisation
mbmg.pensoft.net/article/13207
What is eDNA method standardisation and why do we need it? by Theroux et al.
#Environmental #DNA #lab #accreditation #management #methods #standardisation #edna

Metabarcoding and MetagenomicsWhat is eDNA method standardisation and why do we need it?The rapid advancement of environmental DNA (eDNA) science in the past two decades has inspired a concomitant growth in the development of eDNA sampling and analytical methods. However, these methods are often developed by individual laboratories or institutions, which can isolate protocols within programmes, agencies or regions and prevent the beneficial exchange of data and ideas. Recent efforts to advance national and international coordination have resulted in a groundswell of standardisation efforts, but there is still considerable confusion around the role of formal standards for regulatory or research applications. With this commentary, we hope to provide clarity on the terminology used in standardisation discussions, including the differences between formal standards and best practice guidelines. Additionally, we discuss how eDNA method choice may be informed by environmental management scenarios and review examples of formal eDNA method standards being used to inform management action. The eDNA community now has an opportunity to develop a roadmap for method development to help close standardisation gaps, advance eDNA method adoption and accelerate our ability to monitor biological life at the scales our current environmental challenges demand.
Public *
Aral Balkan

Oh my goodness, how did I miss that in ES7 you can use a closure as a method. Goodbye `bind()`, you will not be missed :)

e.g.,

```js
class A {
b = () => console.log(this)
}

const a = new A()
a.b() // A { b: [Function: b] }

const c = a.b
c() // A { b: [Function:b] }
```

Nice! :)

**Edit**: Be careful with this. See this note by @marsup: mastodon.social/@marsup/113799

MastodonMarsup (@marsup@mastodon.social)@aral@mastodon.ar.al Respectfully, this looks like an anti-pattern. `b` won't be part of the prototype, potentially preventing some meta programming, and you're going to get a new `b` for each instance of that class, consuming that much more memory for each instance you hold.
#JavaScript#EcmaScript7#ES7
Public
Thomas

I recommend reading #JacquesEllul "Le fascisme, fils du libéralisme" ("Fascism, son of Liberalism, 1937).

Ellul was an eye-witness of fascism in Italy, Germany and Spain. He argued that fascism is a method, not an ideology, a technology of the social. By using industrial organization methods it turns a society into a totalitarian enterprise.

An OCRed version of the articler is available on JSTOR (a free account is sufficient)..

#Fascism#systemsthinking#methods
Continued thread
Public
Solarbird :flag_cascadia:

okay yeah this is definitely good

METHODS POST I mean it's trivial but

* put your yeast and sugar into the warm water like always

* let it activate the usual 10 minutes (or however)

* add rounded 1/4 cup onion flakes, stir in well

* let them rehydrate in the mix for 3 minutes

* mix into drys and proceed as usual

trust me on this one if you like onions it's dang good

#baking#bagels#onions
Public
Giuseppe Michieli

Establishing #methods to #monitor #H5N1 #influenza virus in dairy #cattle #milk

Source: MedRxIV, AbstractHighly Pathogenic Avian Influenza strain H5N1 has caused a multi-state outbreak among US dairy cattle, spreading across 15 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk from 20 states for methods development,…

etidioh.wordpress.com/2024/12/

ETIDIoH · Establishing #methods to #monitor #H5N1 #influenza virus in dairy #cattle #milk
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