CEIT Metaverse and Game “ at the Department of Computer Engineering and Information Technology, Faculty Of Engineering"

Galaxy Workflows created at the UFZ

A UCL-based initiative funded by the BBSRC to develop a agri-ecology specific pipeline community using nextflow and nf-core.

Workflows related to CPSM Bioconductor package for multi-omics survival analysis.

Software and data format standards for management of microscopy image data. Joint project between international private and public research

Team working on reproducibility badging for workflows

NCI CCR Collaborative Bioinformatics Resource

Changing the ‘Findable, Accessible, Interoperable and Re-usable’ (FAIR) landscape for UK researchers

The Snakemake-Workflows team develops best practice workflows for Snakemake

Research team focused on spatial transcriptomics analysis in polyploid organisms

Team that built PathoFact 2.0

Workflows for Centre for New Antibacterial Strategies at UiT The Arctic University of Norway

This dataset is an RO-Crate representation of an execution of the tissue/tumor prediction workflow for digital pathology from crs4/deephealth-pipelines. It follows the Provenance Run Crate profile. The workflow has been run with cwltool, using the --provenance option to generate a CWLProv RO bundle, and then converted to an RO-Crate using runcrate. The input dataset is Mirax2-Fluorescence-2 by Yves Sucaet, from the MIRAX test data.

Keçeci Numbers: Keçeci Sayıları

Description / Açıklama

Keçeci Numbers (Keçeci Sayıları): Keçeci Numbers; An Exploration of a Dynamic Sequence Across Diverse Number Sets: This work introduces a novel numerical sequence concept termed "Keçeci Numbers." Keçeci Numbers are a dynamic sequence generated through an iterative process, originating from a specific starting value and an increment value. In each iteration, the increment value is added to the current value, and this "added value" is recorded ...

adnus (AdNuS): Advanced Number Systems

adnus is a Python library that provides an implementation of various advanced number systems. This library is designed for mathematicians, researchers, and developers who need to work with number systems beyond the standard real and complex numbers. Features

Harmonic and Oresme Sequences: Functions to generate harmonic numbers and Oresme sequences. Bicomplex Numbers: A class for bicomplex numbers with full arithmetic support. Neutrosophic Numbers: Classes ...

KececiLayout

Kececi Layout (Keçeci Yerleşimi): A deterministic graph layout algorithm designed for visualizing linear or sequential structures with a characteristic "zig-zag" or "serpentine" pattern.

Python implementation of the Keçeci layout algorithm for graph visualization. Description / Açıklama

This algorithm arranges nodes sequentially along a primary axis and offsets them alternately along a secondary axis. It's particularly useful for path graphs, chains, or showing progression.

Bu ...

Oresmej: Oresme Jax

Oresme numbers refer to the sums related to the harmonic series. Türkçe Tanım:

Oresme Sayıları, 14. yüzyılda Nicole Oresme tarafından incelenen matematiksel serilerdir. Oresme sayıları harmonik seriye ait toplamları ifade eder. İki türü vardır:

( \frac{n}{2^n} ) serisi (Oresme'nin orijinal çalışması), Harmonik sayılar (( H_n = 1 + \frac{1}{2} + \cdots + \frac{1}{n} )). Bu sayılar, analiz ve sayı teorisinde önemli rol oynar.

English Definition:

Oresme Numbers are mathematical ...

Türkçe Tanım:

Oresme Sayıları, 14. yüzyılda Nicole Oresme tarafından incelenen matematiksel serilerdir. Oresme sayıları harmonik seriye ait toplamları ifade eder. İki türü vardır:

( \frac{n}{2^n} ) serisi (Oresme'nin orijinal çalışması), Harmonik sayılar (( H_n = 1 + \frac{1}{2} + \cdots + \frac{1}{n} )). Bu sayılar, analiz ve sayı teorisinde önemli rol oynar.

English Definition:

Oresme Numbers are mathematical series studied by Nicole Oresme in the 14th century. Oresme numbers refer to the sums ...

Keçeci Fractals: Keçeci Fraktals

Keçeci Circle Fractal: Keçeci-style circle fractal.

Description / Açıklama

Keçeci Circle Fractal: Keçeci-style circle fractal.:

This module provides two primary functionalities for generating Keçeci Fractals:

kececifractals_circle(): Generates general-purpose, aesthetic, and randomly colored circular fractals. visualize_qec_fractal(): Generates fractals customized for modeling the (version >= 0.1.1) concept of Quantum Error Correction (QEC) codes. Stratum ...

Keçeci Binomial Squares (Keçeci Binom Kareleri): Keçeci's Arithmetical Square (Keçeci Aritmetik Karesi, Keçeci'nin Aritmetik Karesi)

Description / Açıklama

Keçeci Binomial Squares (Keçeci Binom Kareleri): Keçeci's Arithmetical Square (Keçeci Aritmetik Karesi, Keçeci'nin Aritmetik Karesi):

Keçeci Binomial Squares (Keçeci Binom Kareleri): The Keçeci Binomial Square is a series of binomial coefficients forming a square region within Khayyam (مثلث خیام), Pascal, Binomial Triangle, selected from a ...

grikod2 (Gri Kod, Gray Code)

A Python library for converting binary numbers to Gray Code with ease. Tanım (Türkçe)

Gri Kod: grikod2 İkili sayıları Gri Koda çevirir. Description (English)

Gri Kod: grikod2 converts binary numbers to Gray Code. Kurulum (Türkçe) / Installation (English) Python ile Kurulum / Install with pip, conda, mamba

pip install grikod2 -U python -m pip install -U grikod2 conda install bilgi::grikod2 -y mamba install bilgi::grikod2 -y

• pip uninstall grikod2 -y

• pip install ...

Grikod (Gri Kod, Gray Code)

Tanım (Türkçe) Gri Kod: Grikod İkili sayıları Gri Koda çevirir.

Description (English) Gri Kod: Grikod converts binary numbers to Gray Code.

Kurulum (Türkçe) / Installation (English) Python ile Kurulum / Install with pip, conda, mamba pip install grikod -U python -m pip install -U grikod conda install bilgi::grikod -y mamba install bilgi::grikod -y

• pip uninstall grikod -y

• pip install -U grikod
• python -m pip install -U grikod PyPI

Test Kurulumu / Test Installation ...

This is metadata of human trafficking research conducted by Daniel Tesfa in Tigray and Addis Ababa between October 2024 and March 2025.

Download all genome from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide with filter host:viridiplantae and Refseq on.

This presentation was given at the UK DARIAH day at Edinburgh.

This document provides guidance for understanding and implementing the set of workflows included in this collection. It outlines best practices and recommendations to ensure successful setup and execution of automated and real-time image processing pipelines.

Guidelines for using Scipion in the context of on-the-fly image processing at cryo-EM facilities. This document is divided into three main sections:

• On-the-fly processing: Monitoring data acquisition in real time.

• Processing workflows and templates: Building familiarity with creating and customizing workflows and templates in Scipion.

• Scipion with queue systems: Demonstrating Scipion’s behavior and integration with SLURM-based queueing systems.

This document provides a detailed explanation of all the workflows, including their functionalities, problems they address, advantages, disadvantages, implementation requirements, and open points for future versions.

In the age of high-throughput data, computational workflows have made data processing tasks flexible, manageable, and automated. To administer different computational activities in a workflow, different workflow management systems (WMS) are used that necessitate a sophisticated level of standardisation. Standardisation and reproducibility can be achieved by using standard formats for specifying workflows, such as Common Workflow Language (CWL), and provenance gathering with the standard W3C PROV ...

Poster and presentation video by Ambarish Kumar

This is human trafficking vecabulory that explains how terms are used to explore the human trafficking context in Ethiopia.

ConceptScheme URI https://workflowhub.eu/events/11 PREFIX vocab https://workflowhub.eu/events/11 dct:title Human Trafficking Vocabulary dct:description Welcome to Human Trafficking Vocabulary dct:creater https://orcid.org/0000-0002-5115-0231

URI skos:prefLabel@en skos:altLabel@en skos:definition@en skos:narrower(separator=",") skos:notation@en vocab:type_of_data Data Type ...

Solving the Hamiltonian Problem in Graph Theory Education with Z3 and the Keçeci Layout

Mehmet Keçeci ORCID: https://orcid.org/0000-0001-9937-9839

Received: 08.21.2025

Abstract: Whilst graph theory constitutes a cornerstone of computer science and mathematics education, the abstract nature of NP-complete problems, such as the Hamiltonian cycle problem, presents a significant conceptual challenge for students. An intuitive grasp of such problems often requires the analytical inspection of complex ...

Graf teorisi, bilgisayar bilimleri ve matematik eğitiminin temel taşlarından birini oluşturmakla birlikte, Hamilton döngüsü gibi NP-tam problemlerin soyut doğası, öğrenciler için önemli bir anlama zorluğu teşkil etmektedir. Bu tür problemlerin sezgisel olarak kavranması, genellikle karmaşık ve standart dışı graf yapılarının analitik olarak incelenmesini gerektirir. Geleneksel öğretim metotları, bu karmaşıklığı etkili bir şekilde aktarmada yetersiz kalabilmekte ve öğrencilerin konuya olan ilgisini ...

Hilbert spaces provide the fundamental mathematical framework for describing quantum mechanical systems. Their structure, characterized by an inner product and completeness, allows for the representation of quantum states as vectors and physical observables as self-adjoint operators. Key quantum phenomena such as superposition and entanglement find natural expression within this formalism. Superposition, where a quantum system can exist in multiple states simultaneously, is represented by linear ...

The development of quantum computers represents one of the most exciting and challenging endeavours in modern science. Progress in this field, particularly with the advent of the second quantum revolution, necessitates a profound interplay between diverse disciplines such as materials science, condensed matter physics, and quantum information theory. The primary aim of this work is to explore the potential of layered quantum structures containing exotic particles—Weyl and Majorana fermions—to ...

Keçeci Varsayımı'nın Hesaplanabilirliği: Sonlu Adımda Kararlı Yapıya Yakınsama Sorunu

Mehmet Keçeci ORCID: https://orcid.org/0000-0001-9937-9839, Independent Researcher

Received: 03.08.2025

Abstract:

Bu çalışma, "Keçeci Varsayımı" olarak adlandırılan yeni bir matematiksel hipotezi sunar ve bu varsayımın, klasik Collatz Varsayımı'nın çok daha genel bir çerçevede formüle edilmiş hali olabileceğini ileri sürer. Keçeci Varsayımı, belirli bir yinelemeli süreç boyunca, herhangi bir başlangıç değerinin ...

Bu çalışma, harmonik serilerin hesaplanmasında geleneksel saf Python tabanlı bir yaklaşım ile modern JAX kütüphanesine dayalı bir yaklaşımın performans, ölçeklenebilirlik ve verimlilik açısından karşılaştırılmasını sunmaktadır. Harmonik seri ve matematiksel analizde önemli bir yere sahip olan ıraksak bir seridir. Hesaplamalı matematikte bu tür serilerin etkin bir şekilde değerlendirilmesi, özellikle büyük veri ve yüksek hassasiyet gerektiren uygulamalarda kritik öneme sahiptir. Geleneksel saf ...

The Limits of Python in Computational Mathematics and Their Extension with JAX: An Application on Harmonic Numbers

Mehmet Keçeci ORCID: https://orcid.org/0000-0001-9937-9839, Independent Researcher

Received: 29.07.2025

Abstract:

This study presents a comparative analysis of a traditional, pure Python-based approach and a modern, JAX library-based approach for calculating the harmonic series, focusing on performance, scalability, and efficiency. The harmonic series is a divergent series of significant ...

This study extends the domain of Keçeci Numbers, a unique class of sequences generated by a distinctive algorithm, beyond standard number systems into advanced mathematical structures such as neutrosophic and hyperreal numbers. Keçeci Numbers are sequences produced via a recursive algorithm based on a starting value and an incremental scalar, governed by rules of divisibility and primality. The primary objective of this paper is to investigate the behaviour of this deterministic algorithm within ...

Bu çalışma, özgün bir algoritmik yapıya sahip olan Keçeci Sayı dizilerinin tanım kümesini, standart sayı sistemlerinin ötesine taşıyarak nötrosofik ve hipergerçek sayılar gibi ileri düzey matematiksel yapılarla genişletmektedir. Keçeci Sayıları, temel olarak bir başlangıç değeri ve bir artış skalerine dayanan, bölünebilirlik ve asallık testlerine bağlı özyinelemeli bir algoritma ile üretilen dizilerdir. Bu çalışmanın temel amacı, bu deterministik algoritmanın, belirsizlik (nötrosofik) ve sonsuz ...

This study presents a comparative analysis of static and dynamic number sequences, using the classical Oresme numbers and the novel Keçeci numbers, developed by Mehmet Keçeci, as primary case studies. Static sequences are characterized by a fixed, predictable recurrence relation. The Oresme numbers—the partial sums of the harmonic series (Η_n=∑(k=1)^n 1/k)—exemplify this category. Their generation follows a simple, deterministic rule (Η_n= Η(n-1)+1/n), and their predictable divergence, proven ...

Nodal-line semimetals constitute a fascinating subclass within the family of topological materials in condensed matter physics. These unique materials are characterized by the intersection of their electronic energy bands along one or more closed or open lines within the Brillouin Zone, rather than at isolated points. These lines of intersection are termed "nodal lines," and along these lines, electrons can behave as if they were massless, leading to extraordinary electronic properties. The ...

Weyl semimetals (WSMs) have emerged as one of the most groundbreaking discoveries in condensed matter physics in recent years, deepening our fundamental scientific understanding and opening new horizons for future technologies. These materials are named after Hermann Weyl, who in 1929 predicted Weyl fermions – massless, chiral relativistic particles. WSMs, as low-energy excitations of these fermions in solid-state systems, possess special points in their electronic band structure where bands cross ...

Beyond Topology: Deterministic and Order-Preserving Graph Visualization with the Keçeci Layout

Mehmet Keçeci1 1ORCID : https://orcid.org/0000-0001-9937-9839, İstanbul, Türkiye

Received: 03.07.2025

Özet/Abstract:

The visualization of scientific data is a fundamental step in uncovering hidden patterns and relationships within complex systems. While conventional force-directed graph layout algorithms (e.g., spring layout) are effective at displaying the general topology and clustering tendencies of ...

This study comprehensively examines the profound technological and methodological synergies existing between observations made via interferometric detectors such as LIGO and Virgo, which have revolutionized the field of gravitational wave (GW) astrophysics, and the rapidly advancing quantum computing (QC) technologies. As both disciplines aim to perform measurements pushing the limits of precision, the effective control and mitigation of environmental and quantum-originated noise pose a critical ...

Many systems encountered in nature and engineering exhibit complex and hierarchical geometric structures. Fractal geometry provides a powerful tool for understanding and modeling these structures. However, existing deterministic circle packing fractals, such as the Apollonian gasket, often adhere to fixed geometric rules and may fall short in accurately reflecting the diversity of observed structures. Addressing the need for greater flexibility in modeling physical and mathematical systems, this ...

Keçeci Deterministic Zigzag Layout (Keçeci Zigzag Layout Algorithm, Keçeci Layout) is a deterministic node layout algorithm designed for graph visualization in Python. Its primary purpose is to position the nodes of a graph in a predefined, sequential, and repeatable manner. The algorithm processes nodes sequentially, placing them along a user-defined primary axis (e.g., top-down or left-to-right) while applying an offset on the secondary axis in a zigzag pattern. This zigzag pattern helps prevent ...

This workflow is part of the EJP RD case study on CAKUT published here: Bayjanov, J.R., Doornbos, C., Ozisik, O. et al. Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT. Sci Rep 14, 20731 (2024). https://doi.org/10.1038/s41598-024-71721-8

Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various ...

EXCON (v2.3.1)

A Nextflow pipeline for gene family EXpansion and CONtraction analysis across multiple species using CAFE5.

Given a set of genome assemblies and annotations, EXCON builds orthogroups with OrthoFinder, fits and compares multiple CAFE models to identify gene families evolving at significantly different rates, and automatically selects the best-fitting model for downstream analysis. Optionally, GO enrichment analysis can be run on expanded and contracted gene families, and ...

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

iPSC Data Analysis

Description

This project is part of the Dutch X-omics initiative and focuses on the analysis of multi-omics data from several iPSC lines. The data included genomics, transcriptomics, proteomics, and several different types of metabolomics.

Goal

The goal is to identify disease-specific traits of the patient-derived iPSC compared to various control lines.

Pipeline overview

File outline

|- README.md     # This readme\ |- Data analysis plan.md ...

EATRIS-Plus Multi-omics Analysis Workflow

Analysis workflow used to analyze the cohort of healthy blood donors

Prerequisites

Multi-omics data set from Zenodo

• The data is stored in a Multi_Assay_Experiment object, which is used as input for the workflow
• The object can be downloaded here: https://doi.org/10.5281/zenodo.10782799

Install Nextflow using conda

Create a Conda Environment:

conda create -n nextflow-env 
conda activate nextflow-env 
conda install -c bioconda
...

CPSM: Cancer patient survival model - Workflow

Introduction

CPSM is an R package that provides a comprehensive computational pipeline for predicting survival probabilities and risk groups in cancer patients. It includes dedicated modules to perform key steps such as data preprocessing, training/test splitting, and normalization. CPSM enables feature selection through univariate cox-regression survival analysis, feature selection though LASSO method, and calculates a LASSO-based Prognostic ...

Integrative Prediction Strategy (IPS) predicts brain gene expression from blood-derived features using pre-trained machine learning models. The workflow integrates multiple feature selection strategies (unsupervised and supervised) and evaluates model performance across cross-validation folds.

Workflow Steps:

1. Load matched blood and brain gene expression data.
2. Apply feature selection:

• Unsupervised feature selection (features selected without using the target brain gene)
• Supervised ...

Workflow Overview

This Galaxy workflow allows transferring ARC imaging data stored as .ZIP file to a target OMERO instance by 1) keeping the ARC structure and 2) automatize the metadata annotation of the assay.

How does it works

The workflow extract all the ./assays/experiment/dataset/ file path and create an OMERO dataset containing the images. The "isa.assay.xlsx" file is used to add key-value pairs to the dataset.

Workflow Inputs

The workflow as three different data inputs: ...

RNASeqCompTest

...

This is the source code for an applet that runs on the DNAnexus Platform. This applet calculates the total storage for each user in a given folder in a given project on the UK Biobank Research Analysis Platform (UKB-RAP).

Applet inputs

The applet has three inputs:

1. project: the name of the UKB-RAP project in which to calculate the data storage.
2. folder: the name of the folder in the UKB-RAP project to be searched (if not a top-level folder then the full path should be given e.g., ...

Quantifying the unknown on MS1 level. UnbeQuant allows the quantification of measured ions without identification annotations in a DDA setting for mass spectrometry proteomics data from Bruker or Thermo mass spectrometers. To achieve this it uses identification results and sets same identifications across runs as anchors to align multiple runs, providing a mixture of the following: Identified ions with quantitative values, only some identified ...

CHAMPAGNE 🍾

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

...

The Human–AI Ledger (HAIL) defines a structured, repeatable workflow for human–AI collaboration. Through standardized checkpoints and a session ledger, HAIL documents ethical, creative, and procedural context across both human and AI contributions. While AI-generated outputs are inherently non-deterministic, HAIL supports process reproducibility by providing a consistent framework for recording collaboration, facilitating auditability, transparency, and ethical accountability in co-creative AI ...

Summary

This notebook shows how to integrate genomic and image data resources. This notebook looks at the question Which diabetes related genes are expressed in the pancreas?

Steps:

• Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.
• Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.

We use the intermine Python API ...

POLY_PIPELINE

A data analysis pipeline for STOmics data tailored to polyploid organisms.

Contributing

Contributions are welcome! Please fork the repository and submit a pull request. See the CONTRIBUTING.md for details.

Main Pipeline (Cluster Execution)

The core scripts are optimized for SGE and PBS clusters execution. They use relative paths and must be run from the POLY_PIPELINE main directory.

Data Input

The input file must be the ...

Example showing how to interact with the public bioimaging resources like the Image Data Resource (IDR)

Collection of EC-Earth3 workflows running with Autosubmit 3, with and without task wrappers, for different Slurm-based HPC platforms. See the individual descriptions for further details.

Collections of materials used as part of the Data Steward Curriculum

https://github.com/crim-ca/application-packages

Common Workflow Language definitions that can be employed in the context of OGC API - Processes deployment. Open Geospatial Consortium (OGC) API Processes can leverage CWL to integrate worklows and processes.

Open source Web API bridging OGC API - Processes with CWL by the Computer Research Institute of Montreal / Centre de recherche informatique de Montréal (CRIM): https://github.com/crim-ca/weaver

Collection of workflows exploring data in the Image Data Resource (IDR).

Open Work Flow Articles (OWFAs)

This is an inclusive collection of workflows related to biodiversity and ecology (especially non-microbial). A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). It also aims at collating workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and ...

A collection of image processing templates designed to support data collection and automated processing for Single Particle Analysis (SPA) in cryo-electron microscopy. The workflows range from simple pipelines—including movie alignment, CTF estimation, and quality assessment—to fully automated 2D and 3D processing. Please select the workflow that best suits your needs.

EuCanImage FHIR ETL Implementation

This repository contains the ETL implementation for EuCanImage, encouraging semantic interoperability of the clinical data obtained in the studies by transforming it into a machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create the dictionaries following a FHIR compliant structure.

• Code Language is written in Python 3.11. ...

A set of generic and automatic workflows designed to: 

• Run on-the-fly and unattended.

• Maintain robust stability for a wide range of samples.

• Covers steps from movies to CTF estimation (for the moment).

• Monitor the acquisition process and provide user feedback.

• Comprise three proposed workflows, each with an additional layer of complexity.

TronFlow is an open source collection of computational workflows originally conceived for tumor-normal somatic variant calling over whole exome data and the manipulation of BAM and VCF files with the aim of having comparable and analysis-ready data. Over time, we have extended it to germline variant calling, copy numbers and other related technologies and analyses.

Its modular architecture covers different analytical and methodological use cases that allow analysing FASTQ files into analysis-ready ...