Search Results for "pubmed"
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Showing 67 open source projects for "pubmed"
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JabRef Bibliography Management
Graphical Java application for managing BibTeX and biblatex
JabRef is an open-source, cross-platform citation and reference management tool. Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research. JabRef is available free of charge and is actively developed. It supports you in every step of your research work. -
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MLDatasets.jl
Utility package for accessing common Machine Learning datasets
This package represents a community effort to provide a common interface for accessing common Machine Learning (ML) datasets. In contrast to other data-related Julia packages, the focus of MLDatasets.jl is specifically on downloading, unpacking, and accessing benchmark datasets. Functionality for the purpose of data processing or visualization is only provided to a degree that is special to some datasets. -
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PaperAI
Semantic search and workflows for medical/scientific papers
PaperAI is an open-source framework for searching and analyzing scientific papers, particularly useful for researchers looking to extract insights from large-scale document collections. -
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GROBID
A machine learning software for extracting information
...The extraction here covers the usual bibliographical information (e.g. title, abstract, authors, affiliations, keywords, etc.). References extraction and parsing from articles in PDF format, around .87 F1-score against on an independent PubMed Central set of 1943 PDF containing 90,125 references, and around .89 on a similar bioRxiv set of 2000 PDF (using the Deep Learning citation model). All the usual publication metadata are covered (including DOI, PMID, etc.). -
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ResearchWheel
Research the web without constantly switching tabs.
...With middle click open a wheel with many available actions: 🎓 North | Google Scholar - Search selected text or the webpage title 🧬 North-East |PubMed - Search selected text or the webpage title 📝 East | Append Note - Save selected text to the workspace 📚 South-East |Citation - Generate and copy a citation 📂 South | Workspace - Open the research sidebar 🌐 South-West |Translate - Translate webpage content 🔗 West | Title + URL - Copy a clean Markdown link 📋 North-West | Quote + Source - Copy selected text with source attribution -
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Crossref Author Check
Web app to cross-check publication/authorship against CrossRef
This tool retrieves CrossRef information on article type, authorship, print date, subject area, etc. for publications specified by DOI and/or PubMed IDs (max. 100). The tool also tallies the order of authorship for a specified author. -
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SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
...Milestone: The tool reached about 3000 downloads sine 2012. Article Gemi: PCR primers prediction from multiple alignments. Comparative and functional genomics 2012 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117 A great review on designing primer, Gemi, and other tools: Designing degenerate primers: Overview, challenges, and computational methods. Methods in Microbiology. Vol 57, 2025, Pages 73-89; DOI: 10.1016/bs.mim.2025.01.002 -
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CiteSpace
A widely used tool for visual exploration of scientific literature.
...It can process citation data from popular sources such as the Web of Science, Scopus, Dimensions, and the Lens. CiteSpace also supports basic visual analytic functions for datasets without citation-related information, for example, PubMed, CNKI, ProQuest Dissertations and Theses. CiteSpace reveals how a field of research has evolved, what intellectual turning points are evident along a critical path, and what topics have attracted attention. CiteSpace can be applied repeatedly so as to track the development of a field closely and extensively. The e-book How to Use CiteSpace explains the design principles and functions along with illustrative examples in more detail: https://leanpub.com/howtousecitespace -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
...Ye Q, Singh S, Qian PR, Guo NL. Immune-Omics Networks of CD27, PD1, and PDL1 in Non-Small Cell Lung Cancer. Cancers. 2021;13(17). Epub 2021/09/11. doi: 10.3390/cancers13174296. PubMed PMID: 34503105. -
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Web based cataloging and dedupe application. Highly optimized for processing journal articles. Reads MarcXML and dedupes records using the field 773 combined with a fuzzy search on the title. Written for bibnet.org
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DBSolveOptimum
The software for systems biology/pharmacology modeling
...By this time, DBSolveOptimum has been successfully tested and applied for the development and analysis of both systems pharmacology and conventional PK/PD models of drugs. It is free for academic and industrial use. http://www.ncbi.nlm.nih.gov/pubmed/20698988 -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
... * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018). * PubMed ID: 29562348 * DOI: 10.1093/nar/gky175 -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
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A.I.G.Le is a French PHPMySQL code to simplify lab management. A.I.G.Le means "Aide Interactive a la Gestion de Laboratoire"
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Myelin water atlas
Normative myelin water atlas for myelin distribution in the brain
...The created myelin water atlas with its standard deviation can be used as a reference for your own studies related to myelin. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31347238. -
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MWI spinal cord atlases
Normative atlases for the spinal cord using myelin water imaging
...These atlases (in PAM50 space from Spinal Cord toolbox) can be used as a reference to demonstrate areas of abnormalities in individuals with myelin-related disease and damage. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31407400. -
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MS Data Miner
MS Data Miner - A web-based proteomics software
...The software is described in the following paper: Dyrlund TF, Poulsen ET, Scavenius C, Sanggaard KW, Enghild JJ. MS Data Miner: A web-based software tool to analyze, compare and share mass spectrometry protein identifications. PROTEOMICS 2012 http://www.ncbi.nlm.nih.gov/pubmed/22833312 -
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LOCUST
Custom Sequence Locus Typer
...Publication: Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27; https://www.ncbi.nlm.nih.gov/pubmed/28130240 -
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DualTranscriptDiscovery
Transcript-discovery approach for gene feature delimitation by RNA-seq
...A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model. Biology Open 7(1): bio028498. doi: 10.1242/bio.028498 PMID: 29183907. http://bio.biologists.org/content/7/1/bio028498 https://www.ncbi.nlm.nih.gov/pubmed/?term=29183907 -
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GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
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Pour la médecine fondée sur les faits (Evidence-Based Medicine (EBM)). La technique PICO pour formuler des questions cliniques. Plate-forme web open source pour supporter la création de PICO, la recherche et l'évaluation d'informations.
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Crosshub
Multi-way analysis of The Cancer Genome Atlas (TCGA) project datasets
...RNA-Seq vs. clinical (TNM, stage, follow-up) correlation analysis Generates Excel summaries. For details, see the manual or article G.S. Krasnov et al. NAR 2016, Pubmed ID: 26773058 -
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weinberg-overcluster2
Cluster subsequences of intergenic regions
...It clusters these subsequences based on the output of BLAST comparisons of the IGRs. overcluster2 has been used as part of a method to discover novel non-coding RNA classes. overcluster2 was written by Zasha Weinberg. The basic method was one of the methods described here: https://www.ncbi.nlm.nih.gov/pubmed/19340921 An example of the use of overcluster2 to find non-coding RNAs is here: https://www.ncbi.nlm.nih.gov/pubmed/20230605 -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/ -
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PubData
PubData is a search engine for FTP servers of bioinformatics databases
We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the user's search preferences.