Alternatives to Swiss-PdbViewer
Compare Swiss-PdbViewer alternatives for your business or organization using the curated list below. SourceForge ranks the best alternatives to Swiss-PdbViewer in 2024. Compare features, ratings, user reviews, pricing, and more from Swiss-PdbViewer competitors and alternatives in order to make an informed decision for your business.
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1
HyperProtein
Hypercube
HyperProtein is Hypercube, Inc.'s new product focusing on the computational science associated with protein sequences. The product includes the analysis of one-dimensional protein sequences as well as the analysis of consequent three-dimensional protein structures. In particular, the relationship between sequence and structure is a fundamental facet of the product. Unlike individual software programs that provide capability for some aspect of protein sequence or structure, such as sequence alignment, HyperProtein puts together a multitude of Bioinformatics and Molecular Modeling tools related to the science that initiates with a protein sequence. -
2
Avogadro
Avogadro
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Avogadro is a free, open-source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. -
3
StarDrop
Optibrium
With its comprehensive suite of integrated software, StarDrop™ delivers best-in-class in silico technologies within a highly visual and user-friendly interface. StarDrop™ enables a seamless flow from the latest data through predictive modeling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process. Successful compounds require a balance of many different properties. StarDrop™ guides you through this multi-parameter optimization challenge to target compounds with the best chance of success, saving you time and resources by enabling you to synthesize and test fewer compounds. -
4
Ascalaph Designer
Agile Molecule
Ascalaph Designer is a general-purpose program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs. Molecular geometry optimization with conjugate gradient methods. Shows molecular models in separate windows. Each window has two cameras, which allow the model to be simultaneously visualized from two sides and in different graphic modes. The subwindow can be opened by dragging the splitter in the right corner of each graphical window. Clicking on an atom or bond with the left mouse button slightly changes their color and a brief info about the picked object appears in the status bar. The wire-frame style is convenient for large molecules, particularly, proteins. Drawing is very fast for this style. Finally, CPK wire frame combines the properties of several above styles.Starting Price: Free -
5
BIOVIA Discovery Studio
Dassault Systèmes
Today’s biopharmaceutical industry is marked by complexity: growing market demands for improved specificity and safety, novel treatment classes and more intricate mechanisms of disease. Keeping up with this complexity requires a deeper understanding of therapeutic behavior. Modeling and simulation methods provide a unique means to explore biological and physicochemical processes down to the atomic level. This can guide physical experimentation, accelerating the discovery and development process. BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment. It provides researchers with a complete toolset to explore the nuances of protein chemistry and catalyze discovery of small and large molecule therapeutics from Target ID to Lead Optimization. -
6
YASARA
YASARA
YASARA is a molecular graphics, modeling, and simulation program for Windows, Linux, MacOS, and Android developed in 1993, that finally makes it really easy to answer your questions. With an intuitive user interface, photorealistic graphics, and support for affordable virtual reality headsets, shutter glasses, autostereoscopic displays, and input devices, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software. PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs, making use of GPUs if available. You can push and pull molecules around and work with dynamic models instead of static pictures.Starting Price: Free -
7
PyMOL
PyMOL
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms. Better third-party plugin and custom scripting support. A comprehensive software package for rendering and animating 3D structures. A plug-in for embedding 3D images and animations into PowerPoint presentations. PyMOL is a commercial product, but we make most of its source code freely available under a permissive license. The open-source project is maintained by Schrödinger and ultimately funded by everyone who purchases a PyMOL license. Open access incentive executables. Liberal evaluation policy. Improved fuse command (disallows hypervalent bonds, substitutes monovalent atoms instead of attaching to them) Properties inspector now supports unsetting settings with the “delete” key. Fix workspace disappearing on specific display resolutions. -
8
MolView
MolView
MolView is an intuitive, Open-Source web application to make science and education more awesome! MolView is mainly intended as a web-based data visualization platform. You can use MolView to search through different scientific databases including compound databases, protein databases and spectral databases, and view records from these databases as interactive visualizations using WebGL and HTML5 technologies. This web application is built on top of the JavaScript libraries and online services listed below. The Virtual Model Kit has been a source of inspiration for the birth of this project.Starting Price: Free -
9
ChemDoodle
iChemLabs
ChemDoodle 2D contains thousands of chemistry features, helping you produce the highest quality graphics and saving you hours of work. We spend a very long time scrutinizing the graphics output in ChemDoodle. The software automatically orients bonds in the correct directions, merges bond strokes together, places attributes in the best locations and automatically makes smart decisions that lead to the most beautiful and appealing images. Of course, you can always override the software to your preference. Every component of the graphic is fully customizable. Whether you are looking to control bond widths, arrowhead sizes or shape transparency and color; you are in control. ChemDoodle’s drawing controls are made to clearly model the atoms and bonds they manage. Copious visual feedback is provided. There are also many options for customizing the drawing tools to your preference, including for accessibility concerns.Starting Price: $12.5 per month -
10
ChemOffice
PerkinElmer Informatics
ChemOffice enhances scientists’ personal productivity and helps them do better science by enabling them to organize and explore their compounds, reactions and associated properties so that data can be turned into actionable information, and decisions can be made with greater confidence. ChemDraw for Excel adds chemical intelligence to Excel spreadsheets so that chemists can use Excel’s analysis, sorting and organization tools to further manipulate and enrich sets of compounds and data and explore structure-activity relationships. Chem3D generates 3D models so that chemists can view their compounds in three dimensions to assess shape and properties to maximize activity or specificity. ChemFinder is a chemically-intelligent personal database system that scientists use to organize their compounds and to search for and correlate structures with properties. -
11
GenomeBrowse
Golden Helix
This free tool delivers stunning visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. GenomeBrowse runs as a native desktop application on your computer. No longer do you have to sacrifice speed and interface quality to obtain a consistent cross-platform experience. It was developed with performance in mind to deliver a faster and more fluid browsing experience than any other genome browser available. GenomeBrowse is also integrated into the powerful Golden Helix VarSeq variant annotation and interpretation platform. If you love the visualization experience of GenomeBrowse, check out VarSeq for filtering, annotating, and analyzing your data before utilizing the same visualization interface. GB can display all your alignment data. Looking at all your samples in one view can help you spot contextually relevant findings.Starting Price: Free -
12
Eidogen-Sertanty Target Informatics Platform (TIP)
Eidogen-Sertanty
Eidogen-Sertanty's Target Informatics Platform (TIP) is the world's first structural informatics system and knowledgebase that enables researchers with the ability to interrogate the druggable genome from a structural perspective. TIP amplifies the rapidly expanding body of experimental protein structure information and transforms structure-based drug discovery from a low-throughput, data-scarce discipline into a high-throughput, data-rich science. Designed to help bridge the knowledge gap between bioinformatics and cheminformatics, TIP supplies drug discovery researchers with a knowledge base of information that is both distinct from and highly complementary to information furnished by existing bio- and cheminformatics platforms. TIP's seamless integration of structural data management technology with unique target-to-lead calculation and analysis capabilities enhances all stages of the discovery pipeline. -
13
LatchBio
LatchBio
Stop wresting with cloud infrastructure and broken informatics tools. Start discovering biological insights today. Scientific discovery is bottlenecked by the fragmentation of tooling across biology and bioinformatics teams. We built a harmonized bioinformatics platform between wet lab and dry lab in the cloud to help teams accelerate their R&D. Import raw data from your cloud, your service provider, or your team's instruments. Develop and deploy custom bioinformatics workflows in any language. Stop wrestling with your infrastructure. Easily run any workflow and keep a log of every analysis. Ready-to-go interactive visualizations for NGS data with point-and-click plots. Latch supports integration with your organization’s AWS S3. Access hundreds of terabytes of data in an organic filesystem you are familiar with. Define bioinformatics workflows and dynamically generate no-code interfaces using Python with tunable compute and storage. -
14
OmicsBox
BioBam Bioinformatics S.L.
OmicsBox is a leading bioinformatics solution that offers end-to-end data analysis of genomes, transcriptomes, metagenomes, and genetic variation studies. The application is used by top private and public research institutions worldwide and allows researchers to easily process large and complex data sets, and streamline their analysis process. It is designed to be user-friendly, efficient, and with a powerful set of tools to extract biological insights from omics data. The software is structured in different modules, each with a specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results. The functional analysis module includes the popular Blast2GO annotation methodology and makes OmicsBox particularly suited for non-model organism researchStarting Price: €100/month/seat -
15
SnapGene
SnapGene
Accurately design and simulate cloning procedures. Test complicated projects, catch errors before they happen, and obtain the right constructs the first time. Cloning is easier when you can see what you are doing. The intuitive interface offers you unparalleled visibility into your work, simplifying often complex tasks. SnapGene automates documentation, so you don’t have to. See and share every sequence edit and cloning procedure that led to your final plasmid. Improve your core molecular biology procedures, and improve your results. Master SnapGene and key concepts in cloning with our new online learning center, SnapGene Academy. Containing over 50 video tutorials taught by scientific experts, SnapGene Academy helps you advance your skills across multiple molecular biology courses. SnapGene 7.2 provides a new visualization of primer homodimer structures and enhancements to file management, allowing tabs to be organized in multiple windows using drag and drop.Starting Price: $295 per year -
16
SOPHiA GENETICS
SOPHiA GENETICS
Our global data-sharing network generates clinically actionable insights from data to improve patient outcomes worldwide. SOPHiA GENETICS’ mission is to build the future of AI-assisted medicine. We are integrating multimodal healthcare-omics data, unlocking the existing data silos, and developing machine learning models to produce actionable insights that could eventually support healthcare professionals to improve patient outcomes. The revamped interface, new features, and cutting-edge capabilities are set to further accelerate precision medicine workflows, bringing us another step closer to democratizing data-driven medicine. Powered by AI and machine learning (ML), our global cloud-based platform provides a safe, secure, and instantly accessible environment to standardize, compute, and analyze digital health data, generating insights from complex multimodal data sets that have the potential to improve diagnosis, therapy selection, analysis, and drug development. -
17
Chemaxon Marvin Pro
Chemaxon
Draw and publish chemical structures seamlessly with our web-based chemistry editor. Marvin Pro is a drawing tool that combines our chemically intelligent technology with a clean user interface. Chemists, researchers, and students can convert their thoughts into high-quality visual representations in no time. Marvin Pro handles a large number of objects, chemical structures, arrows, or texts, on a single canvas, and aligns them with precision. Chemical editors shouldn’t be complicated. With our intuitive solution, you can transform your chemical structure ideas into clear visuals. The quality of your chemical drawing should match the effort you put into your research. Marvin Pro allows you to create high-quality visuals that you can then present to your workplace. Let the Marvin Pro canvas become an extension of your mind. Add predefined templates or labels, color your structures, and insert images from external sources. You can even display the structure’s formula. -
18
MoluCAD
New River Kinematics
MoluCAD is a full-featured molecular modeling and visualization tool designed for Windows. It is the result of a three-year National Institutes of Health biomedical technology research project aimed at producing low-cost educational software for chemistry students. The latest version incorporates many advanced features only found in expensive workstation-based modeling packages. Ease of use, premium graphical quality, and computational robustness are the trademarks of MoluCAD. Novice users are able to quickly generate models, view them form any perspective, create reaction animations, and save all data to disk. -
19
MolPad
MolPad
MolPad integrates an interactive chemistry sketcher into any online learning platform. Build open questions about molecular structure and organic chemistry that go beyond just recognizing the right answer. Discover how MolPad can enrich online chemistry education by providing a low code environment for creating dynamic content and smart assessment. With MolPad, we have developed several solutions for interactive and intuitive drawing of structural formulas, enabling the student to practice with topics like chemical naming, functional groups, and Lewis structures in a digital environment. By providing smart feedback based on specific errors, the student can gain more insight than with multiple choice questions. -
20
Schrödinger
Schrödinger
Transform drug discovery and materials research with advanced molecular modeling. Our physics-based computational platform integrates differentiated solutions for predictive modeling, data analytics, and collaboration to enable rapid exploration of chemical space. Our platform is deployed by industry leaders worldwide for drug discovery, as well as for materials science in fields as diverse as aerospace, energy, semiconductors, and electronics displays. The platform powers our own drug discovery efforts, from target identification to hit discovery to lead optimization. It also drives our research collaborations to develop novel medicines for critical public health needs. With more than 150 Ph.D. scientists on our team, we invest heavily in R&D. We’ve published over 400 peer-reviewed papers that demonstrate the strength of our physics-based approaches, and we’re continually pushing the limits of computer modeling. -
21
Chemaxon Design Hub
Chemaxon
A platform that connects scientific rationale, compound design, and computational resources. Chemaxon’s Design Hub for medicinal chemistry from analysis to prioritize ideas. Design Compounds and manage ideas within one platform. A single platform that connects scientific rationale, compound design, and computational resources. Switch from PowerPoint files to graphical and chemically searchable hypotheses that are an integral part of the compound design process. Easily work with your trusted phys-chem properties, computational models, novelty issues, or purchasable compound catalogs in a rich visual environment. Involve your CROs in the compound progression process using this secure online service. Analyze collected evidence from biological assays or experimental structural information, extract SAR, and make new hypotheses for the next optimization iteration. Store your scientific hypotheses in a “designer's ELN” (chemically aware drawing canvases). -
22
BIOVIA
Dassault Systèmes
BIOVIA solutions create an unmatched scientific management environment that can help science-based organizations create and connect biological, chemical and material innovations to improve the way we live. The industry-leading BIOVIA portfolio is focused on integrating the diversity of science, experimental processes and information requirements end-to-end across research, development, QA/QC and manufacturing. Capabilities over the areas of Scientific Informatics, Molecular Modeling/Simulation, Data Science, Laboratory Informatics, Formulation Design, BioPharma Quality & Compliance and Manufacturing Analytics. BIOVIA is committed to enhancing and speeding innovation, increasing productivity, improving quality and compliance, reducing costs and accelerating product development for customers in multiple industries. Manage and connect scientific innovation processes and information across the product lifecycle. -
23
ArgusLab
ArgusLab
ArgusLab is a molecular modeling, graphics, and drug design program for Windows operating systems. It’s getting a little dated by now, but remains surprisingly popular. To date, there are more than 20,000 downloads. ArgusLab is freely licensed. You don’t need to sign anything. You can use as many copies as you need if you are teaching a class where your students might benefit from using ArgusLab. You are not allowed to redistribute ArgusLab from other websites or sources. However, you may link to this website from your own websites if you like. A low-key effort is currently underway to port ArgusLab to the iPad. In addition, I’ve done some work with the Qt cross-platform development environment in an effort to support Mac, PC, and Linux.Starting Price: Free -
24
G6GFINDR System
G6G Tech
g6gTech, Inc. is a software development company that creates in-depth search products in the bioinformatics and artificial intelligence (AI) fields. We have recently changed our name from the G6G Consulting Group to emphasize our focus on creating products. Powered by semantic annotation, the new G6GFINDR System searches an expanding database of bioinformatics and artificial intelligence software using a two-step process that allows you to fine tune your search. The system used the previously developed Directory of Omics and Intelligent Software as a core starting point. We will be expanding the database of searched products at an accelerating rate. All products in the database have been carefully curated. The G6GFINDR System uses cookies to automatically collect information about your activities to optimize results. The G6GFINDR System is created by g6gTech, Inc.Starting Price: $9.95/month/user -
25
QIAGEN CLC Genomics Workbench
QIAGEN Digital Insights
QIAGEN CLC Genomics Workbench is a powerful solution that works for everyone, no matter the workflow. Cutting-edge technology and unique features and algorithms widely used by scientific leaders in industry and academia make it easy to overcome challenges associated with data analysis. User-friendly bioinformatics software solutions allow for comprehensive analysis of your NGS data, including de novo assembly of whole genomes and transcriptomes, resequencing analysis (WGS, WES and targeted panel support), variant calling, RNA-seq, ChIP-seq and DNA methylation (bisulfite sequencing analysis). Analyze your RNA-seq and small RNA (miRNA, lncRNA) data with easy-to-use transcriptomics workflows for differential expression analysis at gene and transcript levels. QIAGEN CLC Genomics Workbench is developed to support a wide range of NGS bioinformatics applications. -
26
Qlucore Omics Explorer
Qlucore
Qlucore Omics Explorer is so easy to use that you no longer have to depend on an expert in bioinformatics to explore and analyze your Omics and NGS data sets. Qlucore Omics Explorer is a D.I.Y next-generation bioinformatics software for research in life science, plant- and biotech industries, as well as academia. The powerful and flexible visualization-based data analysis tool with inbuilt powerful statistics delivers immediate results and provides instant exploration and visualization of big data. The software is developed to allow the workflow which best suits you and your experiments and maximizes the outcome of your research. By combining instant visualization with powerful statistics and flexible selection methods, you will be able to see your results immediately. As a user, you decide your own workflow and starting point. You are in control and can tailor the exploration to meet your specific needs. -
27
Pluto
Pluto Biosciences
Since its founding in 2021 from the Wyss Institute at Harvard University, Pluto has become a trusted partner of life sciences organizations around the country ranging from biotech start-ups to public biopharma companies. Our cloud-based platform gives scientists the ability to manage all of their data, run bioinformatics analyses, and create interactive and publication-quality visualizations. The platform is currently being used for a wide variety of biological applications, from preclinical / translational science research, to cell and gene therapies, drug discovery and development, to clinical research. -
28
Partek Flow
Partek
Partek bioinformatics software delivers powerful statistical and visualization tools in an easy-to-use interface. Researchers of all skill levels are empowered to explore genomic data quicker and easier than ever before. We turn data into discovery®. Pre-installed workflows and pipelines in our intuitive point-and-click interface make sophisticated NGS and array analysis attainable for any scientist. Custom and public statistical algorithms work in concert to easily and precisely distill NGS data into biological insights. Genome browser, Venn diagrams, heat maps, and other interactive visualizations reveal the biology of your next-generation sequencing and array data in brilliant color. Our Ph.D. scientists are always just a phone call away and ready to help with your NGS analysis any time you have questions. Designed specifically for the compute-intensive needs of next-generation sequencing applications with flexible installation and user management options. -
29
VSClinical
Golden Helix
VSClinical allows for the clinical interpretation of variants based on ACMG & AMP guidelines. The VSClinical guided workflow enables following the American College of Medical Genetics (ACMG) guidelines used to identify and classify causal variants for inherited disease risk, cancer predisposition, and the diagnosis of rare diseases. The ACMG/AMP joint guidelines for variant interpretation provide a set of criteria to score variants and place them into one of five classification tiers. Following the guidelines requires deep diving into the annotations, genomic context, and existing clinical assertions about every variant. VSClinical provides a tailored workflow to score each relevant criterion while also providing all the bioinformatic, literature and evidence from clinical knowledgebases to assist in the scoring and interpretation process. VSClinical is designed to allow variant scientists to efficiently process variants. -
30
MEGA
MEGA
MEGA (Molecular Evolutionary Genetics Analysis) is a powerful and user-friendly software suite designed for analyzing DNA and protein sequence data from species and populations. It facilitates both automatic and manual sequence alignment, phylogenetic tree inference, and evolutionary hypothesis testing. MEGA supports a variety of statistical methods including maximum likelihood, Bayesian inference, and ordinary least squares, making it an essential tool for comparative sequence analysis and understanding molecular evolution. MEGA offers advanced features such as real-time caption generation to help explain the results and methods used in analysis and the maximum composite likelihood method for estimating evolutionary distances. The software is equipped with robust visual tools like the alignment/trace editor and tree explorer and supports multi-threading for efficient processing. MEGA can be run on multiple operating systems, including Windows, Linux, and macOS.Starting Price: Free -
31
StrandOmics
Strand Life Sciences
Efficient reporting of NGS-based clinical tests requires a robust and mature platform for automatic variant prioritization, clinical interpretation and report generation. Strand Omics is a fast, HIPAA-compliant cloud-based platform that drives our clinical diagnostics practice. It has been honed over 4 years and over 10,000 clinical reports and multiple peer-reviewed publications. Strand Omics combines bioinformatics algorithms, curated databases, visualization interfaces and reporting capabilities. It has specialized workflows for both rare inherited disorders as well as somatic tumor profiling tests. The platform contains over 10,000 somatic variants curated for oncogenicity, 100 genes curated for druggability in multiple cancer types and 500 drugs curated for evidence in multiple cancer types. -
32
Geneyx
Geneyx
Geneyx Analysis is a comprehensive solution for next-generation sequencing (NGS) data that can scale the process of FASTQ to clinical reports for hospital and commercial labs. This advanced platform integrates machine learning and AI-based features to identify novel biomedical insights, while also improving diagnostic yields and turnaround times. By providing a fully transparent and intuitive solution, Geneyx Analysis enables clinicians and researchers to have complete control over data analysis and alleviates the complexities of regulating in-house bioinformatics pipelines. Protocols can be fully customized to accommodate gene panels, exomes, and genomes, and our comprehensive annotation engine supports the analysis of all genetic variants including structural and copy number variations as well as regulatory elements. Together, Geneyx Analysis automates the diagnostic process from sequencer to report, while creating a comprehensive resource for novel variant discovery. -
33
Bioconductor
Bioconductor
The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists. Resources to maximize the potential of Bioconductor. From basic functionalities to advanced features, our tutorials, guides, and documentation have you covered. Bioconductor uses the R statistical programming language and is open source and open development. It has two releases each year and an active user community. Bioconductor provides Docker images for every release and provides support for Bioconductor use in AnVIL. Founded in 2001, Bioconductor is an open-source software project widely used in bioinformatics and biomedical research. It hosts over 2,000 R packages contributed by over 1,000 developers, with over 40 million downloads per year. Bioconductor has been cited in more than 60,000 scientific publications.Starting Price: Free -
34
Geneious
Geneious
Geneious Prime makes bioinformatics accessible by transforming raw data into visualizations that make sequence analysis intuitive and user-friendly. Simple sequence assembly and easy editing of contigs. Automatic annotation for gene prediction, motifs, translation, and variant calling. Genotype microsatellite traces with automated ladder fitting and peak calling and generates tables of alleles. Beautiful visualizations of annotated genomes and assemblies are displayed in a highly customizable sequence view. Powerful SNP variants analysis, simple RNA-Seq expression analysis, and amplicon metagenomics. Design and test PCR and sequencing primers and create your own searchable primer database. Geneious Biologics is a flexible, scalable, and secure way to streamline your antibody analysis workflows, create high-quality libraries and select the optimal therapeutic candidates.Starting Price: $1,280 per year -
35
L7|ESP
L7 Informatics
L7 Enterprise Science Platform (L7|ESP®) is a unified platform that contextualizes data and eliminates business silos via process orchestration. It's a comprehensive solution that facilitates the digitalization of data and scientific processes in life sciences organizations. L7|ESP has native applications, including L7 LIMS, L7 Notebooks, L7 MES, L7 Scheduling, and more. It can integrate with existing third-party applications, lab instruments, and devices to capture all data in a single data model. It has a low-code/no-code workflow designer and hundreds of pre-built connectors to enable rapid time-to-value and end-to-end automation. By leveraging a single data model, L7|ESP enables advanced bioinformatics, AI, and ML to offer novel scientific and operational insights. L7|ESP addresses data and lab management needs in life sciences, particularly in: ● Research and Diagnostics ● Pharma and CDMO ● Clinical Sample Management Resource Center: l7informatics dot com/resource-center -
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Galaxy
Galaxy
Galaxy is an open source, web-based platform for data-intensive biomedical research. If you are new to Galaxy start here or consult our help resources. You can install your own Galaxy by following the tutorial and choosing from thousands of tools from the tool shed. This instance of Galaxy is utilizing infrastructure generously provided by the Texas Advanced Computing Center. Additional resources are provided primarily on the Jetstream2 cloud via ACCESS, and with support from the National Science Foundation. Quantify, visualize, and summarize mismatches in deep sequencing data. Build maximum-likelihood phylogenetic trees. Phylogenomic/evolutionary tree construction from multiple sequences. Merge matching reads into clusters with TN-93. Remove sequences from a reference that are within a given distance of a cluster. Perform maximum-likelihood estimation of gene essentiality scores.Starting Price: Free -
37
Loupe Browser
10x Genomics
Loupe Browser is a powerful visualization software that provides the intuitive functionality you need to explore and analyze your 10x Genomics Chromium and Visium data. You can also convert your Seurat objects into Loupe Browser files using the LoupeR package. The navigation and interactive functionality of the Loupe Browser interface uses a lung squamous cell carcinoma dataset. The workspace is centered around the view panel in which single points representing cell barcodes are shown in a variety of projections. Each point represents a single barcode, the vast majority of which correspond to a single cell. The default projection is the t-SNE plot created by the cell ranger pipeline, though other projections are available. You can drag the mouse over the cells to reposition the plot and use the mouse wheel or trackpad to zoom in and out. Cluster labels appear as you move your mouse over the plot, which is useful for data that has a high number of precomputed clusters. -
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Genome Analysis Toolkit (GATK)
Broad Institute
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data and bundles the popular Picard toolkit. These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology, but they can be adapted to handle a variety of other technologies and experimental designs.Starting Price: Free -
39
ChemSketch
ACD/Labs
Comprehensive molecular structure drawing and naming. Draw chemical structures and communicate your science. -
40
Structure Elucidator
ACD/Labs
Elucidate complex structures from experimental data with the help of expert algorithms. -
41
ChemDraw
PerkinElmer
Since 1985 ChemDraw® solutions have provided powerful capabilities and integrations to help you quickly turn ideas and drawings into publications you can be proud of. A chemistry communication suite, ChemOffice+ Cloud transforms your chemical drawings into chemical knowledge by facilitating the management, reporting and presenting of your Chemistry research. ChemOffice+ Cloud, is a robust, comprehensive suite, purpose-built to simplify, facilitate, and accelerate chemistry communication. The cloud-native chemistry communication suite builds on the foundations of ChemDraw Professional and adds access to a powerful set of tools to enable scientific research. The mundane task of creating reports to communicate chemical research has become much more efficient with ChemOffice+ Cloud. With powerful capabilities to search, reuse, select, and organize chemical structures and data, chemists can use ChemOffice+ Cloud to create presentation-ready PowerPoint slides and manuscripts. -
42
BioNeMo
NVIDIA
BioNeMo is an AI-powered drug discovery cloud service and framework built on NVIDIA NeMo Megatron for training and deploying large biomolecular transformer AI models at a supercomputing scale. The service includes pre-trained large language models (LLMs) and native support for common file formats for proteins, DNA, RNA, and chemistry, providing data loaders for SMILES for molecular structures and FASTA for amino acid and nucleotide sequences. The BioNeMo framework will also be available for download for running on your own infrastructure. ESM-1, based on Meta AI’s state-of-the-art ESM-1b, and ProtT5 are transformer-based protein language models that can be used to generate learned embeddings for tasks like protein structure and property prediction. OpenFold, a deep learning model for 3D structure prediction of novel protein sequences, will be available in BioNeMo service. -
43
Chemical Computing Group
Chemical Computing Group
Chemical Computing Group (CCG) has a strong reputation for collaborative scientific support. With offices in North America, Europe and Asia, our team of PhD-level scientists works closely with our clients, providing support, hands-on training and scientific advice on a wide range of projects. CCG continuously develops new technologies with its team of mathematicians, scientists and software engineers and through scientific collaborations with customers. -
44
GeoMx Digital Spatial Profiler (DSP)
nanoString
Quickly resolve tissue heterogeneity and the complexity of microenvironments with the GeoMx Digital Spatial Profiler (DSP), the most flexible and robust spatial multi-omic platform for analysis of FFPE and fresh frozen tissue sections. GeoMx is the only spatial biology platform that non-destructively profiles the expression of RNA and protein from distinct tissue compartments and cell populations with an automated and scalable workflow that integrates with standard histology staining. Spatially profile the whole transcriptome and 570+ protein targets separately or simultaneously from your choice of sample inputs: whole tissue sections, tissue microarrays (TMAs), or organoids. Make GeoMx DSP your spatial biology platform of choice for biomarker discovery and hypothesis testing. Decide where to draw the line and let the tissue be your guide with biology-driven profiling that empowers you to choose the tissue microenvironments and cell types that matter most to you. -
45
hc1
hc1
Founded to improve lives with high-value care, hc1 has emerged as the leader in bioinformatics for precision testing and prescribing. The cloud-based hc1 High-Value Care Platform® organizes volumes of live data, including lab results, genomics, and medications, to deliver solutions that ensure that the right patient gets the right test and the right prescription. Today, the hc1 Platform powers solutions that optimize diagnostic testing and prescribing for millions of patients nationally. To learn more about hc1's proven approach to personalizing care while eliminating waste for thousands of health systems, diagnostic laboratories, and health plans, visit www.hc1.com. -
46
BaseSpace Sequence Hub
Illumina
Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing (NGS) operations. As a key component of the BaseSpace Suite, BaseSpace Sequence Hub is a direct extension of your Illumina instruments. Encrypted data flow from the instrument into BaseSpace Sequence Hub, enabling you to manage and analyze your data easily with a curated set of analysis apps. BaseSpace Sequence Hub is powered by Amazon Web Services (AWS). Offers a security-first environment. Enables you to set up runs and monitor instrument run quality. Promotes efficiency by converting sequencing data to a standard format and streaming directly to the cloud. Provides access to computing resources without the capital expenditure of in-house infrastructure. Increases organizational productivity with easy access to a multitude of genomic analysis apps (provided by you, Illumina, or third parties). -
47
Illumina Connected Analytics
Illumina
Store, archive, manage, and collaborate on multi-omic datasets. Illumina Connected Analytics is a secure genomic data platform to operationalize informatics and drive scientific insights. Easily import, build, and edit workflows with tools like CWL and Nextflow. Leverage DRAGEN bioinformatics pipelines. Organize data in a secure workspace and share it globally in a compliant manner. Keep your data in your cloud environment while using our platform. Visualize and interpret your data with a flexible analysis environment, including JupyterLab Notebooks. Aggregate, query, and analyze sample and population data in a scalable data warehouse. Scale analysis operations by building, validating, automating, and deploying informatics pipelines. Reduce the time required to analyze genomic data, when swift results can be a critical factor. Enable comprehensive profiling to identify novel drug targets and drug response biomarkers. Flow data seamlessly from Illumina sequencing systems. -
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ROSALIND
ROSALIND
Generate greater return on research and improve team productivity. Extend private and public data across teams with interactive data visualization. Rosalind is the only multi-tenant SaaS platform designed for scientists. Analyze, interpret, share, plan, validate, and generate new hypotheses. Code-free visualization, AI-powered interpretation, best-in-class collaboration. Scientists of every skill level can benefit from ROSALIND since no programming or bioinformatics skills are required. With powerful downstream analysis and collaboration, ROSALIND is a discovery platform and data hub connecting experiment design, quality control, and pathway exploration. ROSALIND automatically manages tens of thousands of compute cores and petabytes of storage to dynamically scale up and down for every experiment to deliver results. Instantly share results with other scientists across the globe with audit tracking so everyone can focus on the interpretation, not the processing.Starting Price: $3,250 per month -
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Universal Analysis Software (UAS) provides a platform for analyzing and managing forensic genomic data, simplifying complex bioinformatics. The UAS is an all-inclusive solution, containing analysis modules supporting all current ForenSeq workflows including ForenSeq MainstAY, ForenSeq Kintelligence, ForenSeq DNA Signature Prep, ForenSeq mtDNA Whole Genome, and ForenSeq mtDNA Control Region. UAS rapidly generates FASTQ files, performs alignment, and calls forensically relevant variants from NGS data. Extensive testing backs highly reliable variant calls to deliver accurate results in a user-friendly package with no per-seat licenses. Designed specifically for forensic analysts, UAS streamlines handling of base-by-base sequence information and contains a range of features to enable everything from efficient review of everyday STR profiles to detailed analysis of the most challenging samples.
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ruffus
ruffus
Ruffus is a computation pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics. Ruffus is designed to allow scientific and other analyses to be automated with the minimum of fuss and the least effort. Suitable for the simplest of tasks. Handles even fiendishly complicated pipelines which would cause make or scons to go cross-eyed and recursive. No "clever magic", no pre-processing. Unambitious, the lightweight syntax which tries to do this one small thing well. Ruffus is available under the permissive MIT free software license. This permits free use and inclusion even within proprietary software. It is good practice to run your pipeline in a temporary, “working” directory away from your original data. Ruffus is a lightweight python module for building computational pipelines. Ruffus requires Python 2.6 or higher or Python 3.0 or higher.Starting Price: Free