iDNA-ABT – Detecting DNA Methylation with Adaptive Features and Transductive Information Maximization

iDNA-ABT

:: DESCRIPTION

iDNA-ABT is an advanced deep learning model that utilizes adaptive embedding based on bidirectional transformers for language understanding (BERT) together with a novel transductive information maximization (TIM) loss.

::DEVELOPER

iDNA-ABT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD

iDNA-ABT

:: MORE INFORMATION

Citation

Yu Y, He W, Jin J, Cui L, Zeng R, Wei L.
iDNA-ABT : advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization.
Bioinformatics. 2021 Oct 2:btab677. doi: 10.1093/bioinformatics/btab677. Epub ahead of print. PMID: 34601568.

BioAnnote 2.0.0 – Annotate Biomedical Texts by using different high-quality online Resources

BioAnnote 2.0.0

:: DESCRIPTION

BioAnnote is a desktop application is able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase.

::DEVELOPER

SING Group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • java

:: DOWNLOAD

 BioAnnote

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2013 Jul;111(1):139-47. doi: 10.1016/j.cmpb.2013.03.007.
BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments.
López-Fernández H, Reboiro-Jato M, Glez-Peña D, Aparicio F, Gachet D, Buenaga M, Fdez-Riverola F.

BioClass – tool for Biomedical Text Classification

BioClass

:: DESCRIPTION

BioClass is a tool for biomedical text classification. Through it, a researcher can split a document set, directly related with a specific topic, into relevant or irrelevant documents. BioClass also supports several algorithms in order to increase the classification process efficiency and provides a set of powerful interfaces to analyse, filter and compare obtained results. In addition, all the operations than can be performed in BioClass are connected between them, so that the classification process is completely guided.

::DEVELOPER

SING Group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • java

:: DOWNLOAD

 BioClass

:: MORE INFORMATION

pymzML 2.5.0 – Python module to Parse mzML data based on cElementTree

pymzML 2.5.0

:: DESCRIPTION

pymzML is an extension to Python that offers

  • easy access to mass spectrometry (MS) data that allows the rapid development of tools,
  • a very fast parser for mzML data, the standard in mass spectrometry data format
  • a set of functions to compare or handle spectra

::DEVELOPER

CELLULAR AND MOLECULAR FUNCTIONS OF REACTIVE OXYGEN SPECIES

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Python

:: DOWNLOAD

 pymzML

:: MORE INFORMATION

Citation

Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. (2012)
pymzML – Python module for high throughput bioinformatics on mass spectrometry data,
Bioinformatics, doi: 10.1093/bioinformatics/bts066

PIUMet – Network Integration of Untargeted Metabolomics

PIUMet

:: DESCRIPTION

PIUMet is a network-based algorithm for integrative analysis of untargeted metabolomic data. It leverages known metabolic reactions and protein-protein interactions to analyze the ambiguous assignment of metabolomics features and identify disease-associated pathways and hidden components.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pirhaji L, Milani P, Leidl M, Curran T, Avila-Pacheco J, Clish CB, White FM, Saghatelian A, Fraenkel E.
Revealing disease-associated pathways by network integration of untargeted metabolomics.
Nat Methods. 2016 Sep;13(9):770-6. doi: 10.1038/nmeth.3940. Epub 2016 Aug 1. PMID: 27479327; PMCID: PMC5209295.

DRUID 1.02.1 – Deep Relatedness Inference utilizing Identity by Descent

DRUID 1.02.1

:: DESCRIPTION

DRUID combines IBD segments from a set of close relatives to reconstruct the IBD sharing profile of one of their ungenotyped ancestors. It uses this information to estimate relatedness between the ancestor and other more distant relatives.

::DEVELOPER

Williams lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DRUID

:: MORE INFORMATION

Citation:

Ramstetter MD, Shenoy SA, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Mezey JG, Williams AL.
Inferring Identical-by-Descent Sharing of Sample Ancestors Promotes High-Resolution Relative Detection.
Am J Hum Genet. 2018 Jul 5;103(1):30-44. doi: 10.1016/j.ajhg.2018.05.008. Epub 2018 Jun 21. PMID: 29937093; PMCID: PMC6035284.

PIVOT v1.0.1 – Platform for Interactive analysis and Visualization Of Transcriptomics data

PIVOT v1.0.1

:: DESCRIPTION

PIVOT is an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

PIVOT

:: MORE INFORMATION

Citation

Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J.
PIVOT: platform for interactive analysis and visualization of transcriptomics data.
BMC Bioinformatics. 2018 Jan 5;19(1):6. doi: 10.1186/s12859-017-1994-0. PMID: 29304726; PMCID: PMC5756333.

PESS 1.0.0 – Full-scale Protein Fold Recognition using 1NN

PESS 1.0.0

:: DESCRIPTION

PESS (Protein Empirical Structure Space) is a software of sensitive protein fold recognition using an empirical structure space and 1NN.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PESS

:: MORE INFORMATION

Citation

Middleton SA, Illuminati J, Kim J.
Complete fold annotation of the human proteome using a novel structural feature space.
Sci Rep. 2017 Apr 13;7:46321. doi: 10.1038/srep46321. PMID: 28406174; PMCID: PMC5390313.

Glo-DB – Genomic Locus Operations Database

Glo-DB

:: DESCRIPTION

Glo-DB is designed to perform position-based queries of genomic sequence annotations (features). It contains a query language that affords many different types of position searches via command line and graphical user interfaces, and incorporates various visualization tools.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • java
  • Python

:: DOWNLOAD

 Glo-DB

:: MORE INFORMATION

pathrecon – Temporal Reconstruction Algorithm

pathrecon

:: DESCRIPTION

pathrecon is a set of algorithms for estimating temporal orderings from unordered sets of sample elements.

::DEVELOPER

the Magwene lab, the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

 pathrecon

:: MORE INFORMATION

Citation

Magwene, P. M., P. Lizardi, and J. Kim. 2003.
Reconstructing the temporal ordering of biological samples using microarray data.
Bioinformatics 19(7):842-850

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