Catalogue of Romanian Bioinformatics Services - CaRoBioS

- Under development -

CRB is developing the Catalogue of Romanian Bioinformatics Services (CaRoBioS).

By services, CRB means data resources, software tools, training, computing infrastructure, and help desks.

Objectives

Following the model of several ELIXIR Nodes, the development of the CaRoBioS aims to support the bioinformatics ecosystem in Romania by:

• promoting the awareness of services developed by Romanian research groups,
• increasing the domestic and European use of services developed by Romanian research groups,
• providing structured feedback according to a set of review criteria aligned with the FAIR principles
• identifying critical aspects of interoperability to improve existing services, and
• offering indirect support for access to funding to promote the long-term sustainability of essential services.

Inclusion in the CaRoBioS involves the following steps:

1. Submission of a form containing information about the service being developed. Dedicated forms for services other than data resources and software tools will be made available in future editions.

2. A peer-review evaluation by researchers from the diaspora scientific community, based on the following peer-review criteria.

3. Inclusion in the CaRoBioS, based on the suggestions and recommendations of the peer-review committee.

4. Communication of the suggestions and recommendations formulated by the peer reviewers to the contact person.

5. Classification as an ELIXIR Romania Service – Once Romania becomes an ELIXIR Member, a resource may be designated as a core ELIXIR Romania Service, based on its internal evaluation and relevance to the broader European network. This classification could enable access to support for long-term sustainability.

Please contact CRB at contact_crb@bioinfocluster.ro for further information.

Services List

Choice of subject

Type of Service

Name of service	Tag	Type of services
Galaxy Server UVT	A local Galaxy instance hosted by the West University of Timişoara. Viruses Archaebacteria Eubacteria Protista Fungi Plantae Animalia Human	Software tools
AlphaFold-based protein analysis pipeline	Protein analysis pipeline building on the predictions of AlphaFold2. The core functionality of the pipeline is to determine and present different properties based on the protein sequence and the predicted three-dimensional structure. https://ieeexplore.ieee.org/document/10130994 Viruses Archaebacteria Eubacteria Protista Fungi Plantae Animalia Human	Software tools
SAGS DB - Structural Assessment of Glycosylation Site Database	The database for the Structural Assessment of Glycosylation Sites. Viruses Archaebacteria Eubacteria Protista Fungi Plantae Animalia Human	Data resources
Robosample - Molecular Simulation Program based on high-speed robot mechanics	Reliable and user-friendly simulation package for fast biomolecular sampling that does not require extensive expertise in mechanical engineering or in the statistical mechanics of reduced coordinates. Viruses Archaebacteria Eubacteria Protista Fungi Plantae Animalia Human	Software tools
LRRpred - a ML program for accurate detection of LRR motifs in Leucine Rich Repeat proteins and domains	An open-source tool for detecting LRR motifs within leucine-rich repeat proteins. It relies on secondary structure, relative solvent accessibility, and disorder predictions performed using RaptorX-Property, as well as sequence variability profiles generated using HH-suite on the Uniprot20 sequence database. Viruses Archaebacteria Eubacteria Protista Fungi Plantae Animalia Human	Software tools
NLRexpress - a ML program for swift detection of Nod Like Receptors: NLR/CNL/TNL	NLRexpress is a collection of plant NLR-related motif ML predictors. It includes the following modules: CCexpress, TIRexpress, NBSexpress, and LRRexpress. Not limited to plant NLRs, the LRR module was also developed to screen other LRR-containing protein classes, regardless of their taxonomy. Viruses Archaebacteria Eubacteria Protista Fungi Plantae Animalia Human	Software Tools
molecularmodels.ro	A collection of 3D printable models of various proteins and complexes relevant for teaching biomolecular structures. Instructions on how to convert PDB files to printable STL files and on how to print molecular models are provided. Details available in: Mihasan, M. A Beginner’s Guideline for Low-cost 3D Printing of Macromolecules Usable for Teaching and Demonstration. Biochem. Mol. Biol. Educ. 2021, bmb.21493. Viruses Archaebacteria Eubacteria Protista Fungi Plantae Animalia Human	Training
GitHub - TracyRage/muddy_mine	A mining pipeline - muddy_mine, which could engage NLP technology in the niche environmental topics such as mud volcanoes. This pipeline is able to mine taxonomy (bacterial, archaeal), methods or any other tokens of interest from the Open Access articles. Articles available in the S2ORC database, CC BY-NC 2.0, unmodified (Lo et al. 2020). muddy_mine output represents a csv table with all the relevant data regarding mud volcanoes. Archaebacteria Eubacteria	Data resources
muddy_db - mud volcano database	Interdisciplinary muddy volcano database. Archaebacteria Eubacteria	Data resources

* Related links take you to the related pages in three ELIXIR registries:

bio.tools : a registry of software metadata and descriptions.
FAIRsharing : a registry of databases, standards and policies.
TeSS : a registry of events, training courses and training materials.