Alternatives to HyperProtein

Avogadro serves as a sophisticated molecular editor and visualizer that operates across multiple platforms, catering to fields such as computational chemistry, molecular modeling, bioinformatics, and materials science. With its ability to provide flexible, high-quality rendering alongside a robust plugin architecture, it enhances user experience significantly. This free, open-source tool is compatible with Mac, Windows, and Linux, making it accessible to a wide range of users in scientific disciplines. Its design emphasizes not only functionality but also adaptability to various research needs.

Swiss-PdbViewer, also known as DeepView, is a software tool that offers an intuitive interface for the simultaneous analysis of multiple proteins. Users can superimpose these proteins to determine structural alignments and evaluate various critical components, such as active sites. The application simplifies the process of obtaining information on amino acid mutations, hydrogen bonds, angles, and atomic distances through its easy-to-navigate graphical and menu-driven interface. Developed by Nicolas Guex since 1994, Swiss-PdbViewer was originally closely integrated with SWISS-MODEL, an automated homology modeling server created by the Swiss Institute of Bioinformatics (SIB) within the Structural Bioinformatics Group at the Biozentrum in Basel. Over time, the SWISS-MODEL web interface has progressed significantly, allowing for direct use in advanced modeling tasks. As a result, the complexity of maintaining a direct connection with Swiss-PdbViewer has led to the discontinuation of support for that integration. This evolution reflects broader changes in bioinformatics tools and their capabilities.

Evo 2 represents a cutting-edge genomic foundation model that excels in making predictions and designing tasks related to DNA, RNA, and proteins. It employs an advanced deep learning architecture that allows for the modeling of biological sequences with single-nucleotide accuracy, achieving impressive scaling of both compute and memory resources as the context length increases. With a robust training of 40 billion parameters and a context length of 1 megabase, Evo 2 has analyzed over 9 trillion nucleotides sourced from a variety of eukaryotic and prokaryotic genomes. This extensive dataset facilitates Evo 2's ability to conduct zero-shot function predictions across various biological types, including DNA, RNA, and proteins, while also being capable of generating innovative sequences that maintain a plausible genomic structure. The model's versatility has been showcased through its effectiveness in designing operational CRISPR systems and in the identification of mutations that could lead to diseases in human genes. Furthermore, Evo 2 is available to the public on Arc's GitHub repository, and it is also incorporated into the NVIDIA BioNeMo framework, enhancing its accessibility for researchers and developers alike. Its integration into existing platforms signifies a major step forward for genomic modeling and analysis.

Evo Designer is a cutting-edge tool created by the Arc Institute, harnessing the power of the Evo 2 genomic foundation model to aid in the generation and analysis of DNA sequences. Users can enter nucleotide sequences or select specific organisms, prompting the model to produce relevant DNA sequences tailored to their needs. This platform also offers detailed annotations of coding regions and provides 3D protein visualizations for prokaryotic sequences through ESMFold, enhancing the understanding of protein structures. In addition to these features, Evo Designer evaluates sequences by calculating their perplexity and per-nucleotide entropy, which helps researchers gauge the complexity and variability of the sequences they are working with. The Evo 2 model at the core of this tool has been trained on an impressive dataset of over 9 trillion nucleotides sourced from a wide variety of prokaryotic and eukaryotic genomes. Utilizing a sophisticated deep learning architecture, it models biological sequences with single-nucleotide precision and boasts a context window that can extend up to 1 million tokens, thereby ensuring high accuracy in sequence representation and analysis. This combination of features makes Evo Designer an invaluable resource for genetic research and exploration.

BIOVIA solutions foster an unparalleled environment for scientific management, enabling organizations focused on science to develop and interlink innovations in biology, chemistry, and materials to enhance our quality of life. The leading BIOVIA portfolio emphasizes the seamless integration of diverse scientific disciplines, experimental workflows, and information needs throughout the entire spectrum of research, development, quality assurance, quality control, and manufacturing. It boasts capabilities spanning Scientific Informatics, Molecular Modeling and Simulation, Data Science, Laboratory Informatics, Formulation Design, BioPharma Quality and Compliance, as well as Manufacturing Analytics. BIOVIA is dedicated to accelerating innovation, boosting productivity, enhancing quality and compliance, lowering costs, and expediting product development for clients across various sectors. Additionally, it plays a crucial role in managing and unifying scientific innovation processes and information throughout the entire product lifecycle, ensuring a comprehensive approach to scientific advancement.

Comprehensive molecular structure drawing. Draw chemical structures and communicate your science.

ChemOffice significantly boosts the efficiency of scientists by providing tools that allow them to systematically organize and investigate their compounds, reactions, and relevant properties, transforming raw data into valuable insights that facilitate more informed decision-making. Additionally, ChemDraw for Excel integrates chemical data into Excel, empowering chemists to leverage Excel's analytical capabilities to sort, organize, and enrich their compound datasets while investigating structure-activity relationships. Meanwhile, Chem3D allows chemists to create three-dimensional models of their compounds, enabling them to examine the spatial arrangement and properties of these molecules to optimize their efficacy or selectivity. Furthermore, ChemFinder functions as an intelligent personal database, assisting scientists in managing their compound collections and enabling them to search and correlate chemical structures with their properties effectively. This comprehensive suite of tools collectively streamlines the workflow for researchers, enhancing their ability to conduct high-quality scientific work.

MEGA, which stands for Molecular Evolutionary Genetics Analysis, is an intuitive and highly capable software suite tailored for examining DNA and protein sequence information from various species and populations. It allows for both automated and manual alignment of sequences, the construction of phylogenetic trees, and the testing of evolutionary theories. The software employs an array of statistical approaches such as maximum likelihood, Bayesian inference, and ordinary least squares, making it indispensable for comparative sequence analysis and insights into molecular evolution. Additionally, MEGA includes sophisticated functionalities like real-time caption generation to clarify the findings and methodologies applied during analysis, alongside the maximum composite likelihood method for calculating evolutionary distances. The program is enhanced with powerful visual aids, including an alignment/trace editor and a tree explorer, while also supporting multi-threading to optimize processing efficiency. Furthermore, MEGA is compatible with several operating systems, such as Windows, Linux, and macOS, ensuring accessibility for a diverse user base. In summary, MEGA stands out as a comprehensive tool for researchers delving into the intricacies of molecular genetics.

To reduce attrition rates for molecular entities that are unlikely succeed in nomination as drug candidates, direct new compound synthesizers, and focus animal testing requirements, calculate drug toxicity and safety.

Eidogen-Sertanty's Target Informatics Platform (TIP) stands out as the pioneering structural informatics system and knowledgebase that empowers researchers to explore the druggable genome through a structural lens. By harnessing the burgeoning wealth of experimental protein structure data, TIP revolutionizes structure-based drug discovery, shifting it from a limited, low-throughput field to a dynamic and data-rich scientific discipline. It is specifically designed to connect the realms of bioinformatics and cheminformatics, providing drug discovery scientists with a repository of insights that are not only unique but also highly synergistic with the information available from traditional bio- and cheminformatics tools. The platform's innovative combination of structural data management with advanced target-to-lead calculation and analytical capabilities significantly enhances every phase of the drug discovery process. With TIP, researchers are better equipped to navigate the complexities of drug development and make informed decisions.

Efficient data management and streamlined bioinformatics solutions are essential for laboratories that are either just beginning or rapidly expanding their next-generation sequencing (NGS) capabilities. As an integral part of the BaseSpace Suite, BaseSpace Sequence Hub serves as a seamless extension to your Illumina instruments. The encrypted data transmission from these instruments into BaseSpace Sequence Hub simplifies the management and analysis of your data through a selection of specialized analysis applications. Built on the robust Amazon Web Services (AWS), BaseSpace Sequence Hub prioritizes security, ensuring a safe environment for your data. It allows users to initiate sequencing runs and monitor the quality of instrument operations effectively. This system enhances productivity by converting sequencing data into a standardized format and facilitating direct cloud streaming. Additionally, it grants access to necessary computational resources without the need for significant investments in on-premises infrastructure. Ultimately, it boosts organizational efficiency by providing easy access to a wide array of genomic analysis applications, whether developed by you, Illumina, or third-party providers, thus fostering innovation and progress in genomic research.

MolPad seamlessly incorporates an interactive chemistry sketching tool into various online educational platforms. It allows educators to create open-ended questions regarding molecular structures and organic chemistry that extend beyond simply identifying correct answers. Explore how MolPad enhances online chemistry instruction through a low-code framework that facilitates the development of engaging content and intelligent assessments. Our platform has introduced multiple solutions for the intuitive drawing of structural formulas, allowing students to engage with concepts such as chemical nomenclature, functional groups, and Lewis structures in a digital setting. By offering targeted feedback based on individual mistakes, students can achieve a deeper understanding compared to traditional multiple-choice formats, ultimately fostering a richer learning experience in chemistry. Additionally, this interactive approach encourages students to think critically and creatively about chemical concepts.

Expert algorithms can help you to understand complex structures using experimental data.

StarDrop™, a comprehensive suite of integrated software, delivers the best in silico technology within a highly visual interface. StarDrop™, which allows seamless flow between the latest data, predictive modeling, and decision-making regarding the next round or synthesis, improves the speed, efficiency and productivity of the discovery process. A balance of different properties is essential for successful compounds. StarDrop™, which guides you through the multi-parameter optimization challenge, helps you target compounds with the highest chance of success. It also saves you time and resources by allowing you to synthesize fewer compounds and test them less often.

Profluent's innovative platform transforms the field of protein design by seamlessly combining cutting-edge AI technology with its own experimental capabilities, allowing for the development of proteins that are either inspired by nature or entirely newly conceived. This comprehensive methodology provides precise, flexible, and scalable solutions to intricate biological problems, resulting in advancements that push the boundaries of protein functionality. Profluent's foundational models extend protein design beyond the constraints of traditional random approaches, enabling the simultaneous optimization of various characteristics, enhancing sequence diversity, and unlocking new functionalities. By venturing into unexplored protein territories, Profluent presents distinctive opportunities that surpass the limitations of natural or patented proteins, streamlining the process for partners to achieve commercial viability in a more cost-effective and accessible manner. Underpinning Profluent's capabilities is a strong dedication to scientific excellence, utilizing a wide range of datasets and advanced AI techniques to address complex challenges effectively. As a result, Profluent not only advances protein engineering but also sets a new standard in the industry, fostering innovative collaborations and breakthroughs.

Geneyx Analysis offers an all-encompassing solution for managing next-generation sequencing (NGS) data, efficiently transforming FASTQ files into clinical reports tailored for both hospital and commercial laboratories. This cutting-edge platform incorporates machine learning and artificial intelligence capabilities to uncover new biomedical insights, enhancing diagnostic efficiency and reducing turnaround times. By delivering a fully transparent and user-friendly interface, Geneyx Analysis empowers clinicians and researchers with complete control over data interpretation and simplifies the challenges associated with managing in-house bioinformatics workflows. Users can customize protocols to suit various gene panels, exomes, and genomes, while our extensive annotation engine facilitates the analysis of all genetic variants, including structural and copy number variations, as well as regulatory elements. In combination, Geneyx Analysis streamlines the diagnostic journey from sequencer output to finalized report, while also serving as a valuable resource for the discovery of novel variants. This platform not only enhances clinical capabilities but also paves the way for groundbreaking research in genomics.

Universal Analysis Software (UAS) is a comprehensive platform that facilitates the analysis and management of forensic genomic data, making intricate bioinformatics tasks easier to navigate. This robust solution encompasses a variety of analysis modules that are compatible with all existing ForenSeq workflows, such as ForenSeq MainstAY, ForenSeq Kintelligence, ForenSeq DNA Signature Prep, ForenSeq mtDNA Whole Genome, and ForenSeq mtDNA Control Region. With UAS, users can swiftly generate FASTQ files, execute alignment processes, and identify forensically significant variants from next-generation sequencing (NGS) data. The software's extensive validation ensures highly dependable variant calls, providing precise outcomes in an accessible format without the burden of per-seat licensing fees. Tailored specifically for forensic analysts, UAS optimizes the management of base-by-base sequence data, offering a wide array of features that support everything from the efficient review of standard STR profiles to in-depth analysis of the most complex samples, thus enhancing the overall efficiency of forensic investigations.

The QIAGEN CLC Geneomics Workbench is a powerful tool that works for all workflows. It is easy to overcome data analysis challenges with cutting-edge technology, unique features and algorithms that are widely used by scientists in industry and academia. Bioinformatics software solutions that are user-friendly allow for comprehensive analysis and interpretation of your NGS data. This includes de novo assembly and transcriptome assembly, resequencing analysis, WES and targeted panel support, variant calling, variant calling, RNA–seq, ChIP–seq and DNA methylation analysis (bisulfite sequence analysis). You can analyze your RNA-seq (miRNA, smallRNA) and smallRNA (lncRNA), data using easy-to-use transcriptomics workflows that allow for differential expression analysis at both gene and transcript levels. QIAGEN CLC Genomics Workbench was designed to support a wide variety of NGS bioinformatics programs.

Ascalaph Designer is a versatile software designed for conducting molecular dynamic simulations. It integrates various implementations of molecular dynamics alongside classical and quantum mechanics methodologies from widely-used programs within a unified graphical interface. The software includes molecular geometry optimization utilizing conjugate gradient techniques. Molecular models are displayed in distinct windows, each equipped with dual camera views that enable simultaneous visualization from multiple angles and in various graphic representations. Users can easily open additional subwindows by adjusting the splitter located in the corner of each graphical display. By clicking an atom or bond with the left mouse button, users can slightly alter its color, and relevant information about the selected object is presented in the status bar. The wire-frame visualization style proves especially effective for large molecules, such as proteins, ensuring rapid rendering. Additionally, the CPK wire frame style effectively merges characteristics from several other visualization options, enhancing user experience. This program not only facilitates complex simulations but also significantly improves the analysis of molecular structures through its innovative display features.

PyMOL is a molecular visualization system that operates on a user-sponsored, open-source basis, with oversight and distribution managed by Schrödinger. The PyQt interface has replaced Tcl/Tk and MacPyMOL across all platforms, enhancing the user experience significantly. This software offers improved support for third-party plugins and custom scripting, making it a comprehensive tool for rendering and animating three-dimensional structures. Additionally, it includes a plug-in that allows users to incorporate 3D images and animations directly into PowerPoint presentations. Although PyMOL is a commercial product, the majority of its source code is accessible for free under a permissive license. This open-source initiative is sustained by Schrödinger and primarily funded through the sales of PyMOL licenses. Users benefit from open access to executables and a flexible evaluation policy. Recent updates feature an improved fuse command that prevents hypervalent bonds and replaces them with monovalent atoms instead, along with a properties inspector that now allows users to unset settings using the “delete” key. Furthermore, issues regarding the workspace disappearing at certain display resolutions have also been resolved, contributing to a more seamless experience for users.

The biopharmaceutical sector today is characterized by its intricacy, driven by increasing demands for enhanced specificity and safety, the emergence of new treatment classes, and the complexity of disease mechanisms. To navigate this intricate landscape, a profound comprehension of therapeutic dynamics is essential. Advanced modeling and simulation techniques offer a distinctive approach to investigate biological and physicochemical phenomena at the atomic scale. This methodology not only informs physical experimentation but also expedites the drug discovery and development phases. BIOVIA Discovery Studio integrates more than three decades of peer-reviewed research with cutting-edge in silico methodologies, including molecular mechanics, free energy assessments, and biotherapeutics developability, all within a unified framework. By equipping researchers with a comprehensive suite of tools, it facilitates a deeper examination of protein chemistry, thereby accelerating the discovery of both small and large molecule therapeutics, from Target Identification all the way through to Lead Optimization. Ultimately, this synergy of research and technology underscores the vital role of innovative tools in transforming biopharmaceutical advancements.

MolView is an engaging, open-source web tool designed to enhance the realms of science and education! Primarily, it serves as a platform for visualizing data online. Users can explore various scientific databases, such as those containing compounds, proteins, and spectra, and interact with the information presented through dynamic visualizations enabled by WebGL and HTML5 technologies. The development of this web application relies on several JavaScript libraries and online services. Additionally, the Virtual Model Kit has played a pivotal role in inspiring the creation of this innovative project, pushing the boundaries of how scientific data can be represented and understood. Ultimately, MolView aims to make scientific exploration more accessible and enjoyable for everyone.

Geneious Prime enhances access to bioinformatics by converting raw datasets into intuitive visual representations that facilitate sequence analysis in a user-friendly manner. It offers straightforward sequence assembly along with the convenient editing of contigs. Users benefit from automatic gene prediction, motif identification, translation, and variant calling through its annotation features. It also allows for the genotyping of microsatellite traces using automated ladder fitting and peak calling, producing comprehensive tables of alleles. The platform showcases beautifully designed visualizations of annotated genomes and assemblies, presented in a customizable sequence view that enhances user experience. Furthermore, it supports powerful analyses of SNP variants, simplifies RNA-Seq expression evaluations, and assists in amplicon metagenomics. Users can also design and test PCR and sequencing primers while developing their own searchable primer database. Additionally, Geneious Biologics provides a versatile, scalable, and secure solution to optimize workflows for antibody analysis, enabling the creation of high-quality libraries and the selection of the most suitable therapeutic candidates. This integration of tools fosters greater efficiency and innovation in biological research.

YASARA is a versatile molecular graphics, modeling, and simulation software that was introduced in 1993 and is compatible with Windows, Linux, MacOS, and Android platforms, designed to simplify the process of obtaining answers to your scientific inquiries. Featuring a user-friendly interface and stunning photorealistic visuals, it also accommodates budget-friendly virtual reality headsets, shutter glasses, and autostereoscopic displays, fostering an immersive experience that allows users to concentrate on their objectives while minimizing distractions from the software itself. At the core of YASARA is PVL (Portable Vector Language), an innovative development framework that delivers performance capabilities that far exceed those of conventional applications. This advanced framework empowers users to visualize even the most complex protein structures and facilitates genuine interactive real-time simulations with precise force fields on standard computing systems, while also leveraging GPU capabilities when available. By enabling users to manipulate molecules actively and engage with dynamic models instead of just viewing static images, YASARA represents a significant advancement in molecular modeling technology. This dynamic interaction not only enhances the learning experience but also encourages deeper exploration of molecular behavior.

Partek bioinformatics software offers robust statistical and visualization capabilities through a user-friendly interface that caters to researchers of varying expertise. This innovation allows users to navigate genomic data with unprecedented speed and ease, truly embodying our motto, "We turn data into discovery®." With pre-installed workflows and pipelines in a simple point-and-click format, even complex NGS and array analyses become accessible to all scientists. Our combination of custom and public statistical algorithms works seamlessly to transform NGS data into valuable biological insights. Engaging visual tools like genome browsers, Venn diagrams, and heat maps illuminate the intricacies of next-generation sequencing and array data with vibrant clarity. Additionally, our team of Ph.D. scientists is always available to provide support for NGS analyses whenever queries arise. Tailored to meet the demanding computational requirements of next-generation sequencing, the software also offers flexible options for installation and user management, ensuring a comprehensive solution for research needs. As a result, users can focus more on their research and less on technical challenges.

IPA can also help analyze small-scale experiments that produce gene and chemical lists. IPA allows for targeted searches on genes, chemicals, and drugs. It also allows the creation of interactive models of experimental system. Data analysis and search capabilities allow for the understanding of the significance of data, targets, or candidate biomarkers within larger biological or chemical systems. The Ingenuity Knowledge Base contains highly structured, detail-rich chemical and biological findings that backs the software. Learn more about QIAGEN Ingenuity Pathway Analysis. Comparison Analysis determines which pathways, upstream regulators and diseases are most important. It can also be used to identify biological functions across time, doses, and other conditions.

Manage, store, and collaborate on multi-omic datasets effectively. The Illumina Connected Analytics platform serves as a secure environment for genomic data, facilitating the operationalization of informatics and the extraction of scientific insights. Users can effortlessly import, construct, and modify workflows utilizing tools such as CWL and Nextflow. The platform also incorporates DRAGEN bioinformatics pipelines for enhanced data processing. Securely organize your data within a protected workspace, enabling global sharing that adheres to compliance standards. Retain your data within your own cloud infrastructure while leveraging our robust platform. Utilize a versatile analysis environment, featuring JupyterLab Notebooks, to visualize and interpret your data. Aggregate, query, and analyze both sample and population data through a scalable data warehouse, which can adapt to your growing needs. Enhance your analysis operations by constructing, validating, automating, and deploying informatics pipelines with ease. This efficiency can significantly decrease the time needed for genomic data analysis, which is vital when rapid results are essential. Furthermore, the platform supports comprehensive profiling to uncover novel drug targets and identify biomarkers for drug response. Lastly, seamlessly integrate data from Illumina sequencing systems for a streamlined workflow experience.

Created within the Data Sciences Platform at the Broad Institute, this comprehensive toolkit provides an extensive array of features primarily aimed at variant discovery and genotyping. With its robust processing engine and high-performance computing capabilities, it is equipped to manage projects of any magnitude. The GATK has established itself as the industry benchmark for detecting SNPs and indels in both germline DNA and RNA sequencing data. Its functionalities are now broadening to encompass somatic short variant detection as well as addressing copy number variations (CNV) and structural variations (SV). Besides the core variant callers, the GATK incorporates numerous utilities for executing associated tasks, including the processing and quality assurance of high-throughput sequencing data, and it comes bundled with the well-known Picard toolkit. Originally designed for exome and whole genome data generated via Illumina sequencing technology, these tools are versatile enough to be modified for use with various other technologies and study designs. As research evolves, the adaptability of the GATK ensures it remains relevant in diverse genomic investigations.

Designing and simulating cloning procedures with precision is essential for successful outcomes; testing complex projects can help identify potential errors in advance, ensuring that the correct constructs are generated on the first attempt. The process of cloning becomes significantly more manageable when users have clear visibility into their work, thanks to an intuitive interface that streamlines intricate processes. With SnapGene, documentation is automated, relieving users of the burden of manual record-keeping while allowing them to view and share every alteration made during sequence edits and cloning procedures that ultimately resulted in the final plasmid. Enhancing your core molecular biology techniques can lead to better experimental results, and by mastering SnapGene along with essential cloning concepts through the SnapGene Academy, you can elevate your expertise. This online learning platform features over 50 video tutorials conducted by experienced scientific professionals, enabling you to broaden your knowledge across a range of molecular biology subjects. Additionally, the recent SnapGene 7.2 update introduces improved visualization of primer homodimer structures and enhances file management, allowing for better organization of tabs across multiple windows through a user-friendly drag-and-drop feature. This makes it easier than ever to manage your cloning projects efficiently and effectively.

g.nome is a cloud-native platform designed to offer efficient, scalable, and interoperable workflows tailored for next-generation sequencing analysis. It features a low-code/no-code approach to building pipelines, allowing users to access a curated library of pre-built workflows and toolkits. This empowers researchers to easily import their custom code, manage large datasets with confidence, and enhance collaboration among team members, regardless of their location. By utilizing g.nome, researchers can eliminate longstanding obstacles related to workflow languages, visibility of process flows, and quality assurance. Consequently, they can concentrate entirely on their scientific endeavors, as g.nome transforms the complexities of genomic workflows into streamlined, efficient processes. This innovative platform not only simplifies research but also fosters an environment where scientific inquiry can thrive unhindered.

Qlucore Omics Explorer is designed to be user-friendly, eliminating the necessity to rely on bioinformatics experts for the exploration and analysis of your Omics and NGS datasets. This software serves as a do-it-yourself solution for next-generation bioinformatics in life sciences, plant and biotechnology sectors, and educational institutions. It features a robust and adaptable visualization-based data analysis tool that incorporates advanced statistical methods, yielding instant results and enabling immediate exploration and visualization of extensive data sets. Built to accommodate workflows that align with your research needs, it enhances the effectiveness of your studies. By merging real-time visualization with sophisticated statistical techniques and flexible selection options, you can promptly observe your findings. As a user, you have the autonomy to determine your own workflow and starting point, allowing for a customized exploration that aligns with your unique requirements. This level of control empowers researchers to tailor their analyses, ensuring that the software adapts seamlessly to diverse experimental designs.

Efficiently address tissue heterogeneity and the intricacies of microenvironments using the GeoMx Digital Spatial Profiler (DSP), which stands out as the most versatile and powerful spatial multi-omic platform for examining both FFPE and fresh frozen tissue sections. Unique among spatial biology platforms, GeoMx allows for non-destructive profiling of RNA and protein expression across various tissue compartments and cell populations, supported by an automated and scalable workflow that seamlessly integrates with conventional histology staining. You can spatially profile the entire transcriptome along with over 570 protein targets, either separately or concurrently, utilizing sample inputs such as whole tissue sections, tissue microarrays (TMAs), or organoids. By choosing GeoMx DSP, you position yourself at the forefront of spatial biology for effective biomarker discovery and hypothesis validation. With the ability to determine the relevant boundaries, you can rely on biology-driven profiling that enables you to focus on the tissue microenvironments and cell types that hold the most significance for your research. This innovative approach ensures that your analyses are both comprehensive and tailored to the specific biological contexts of interest.

Enhance research outcomes while boosting team efficiency by utilizing interactive data visualization to extend both private and public datasets among various teams. Rosalind stands out as the sole multi-tenant SaaS platform tailored for scientists, enabling the analysis, interpretation, sharing, planning, validation, and generation of new hypotheses with ease. It offers code-free visualization and employs AI for interpretation, fostering top-tier collaboration among users. Regardless of their expertise, scientists can leverage ROSALIND effectively, as it requires no programming or bioinformatics knowledge. The platform serves as a robust discovery tool and data hub, seamlessly integrating experiment design, quality control, and pathway analysis. ROSALIND's advanced infrastructure automatically orchestrates tens of thousands of compute cores and manages petabytes of storage, scaling resources dynamically for each experiment to ensure timely results. Furthermore, scientists can effortlessly share their findings with peers worldwide, complete with audit tracking to prioritize interpretation over data processing, thereby fostering a more collaborative research environment. This unique combination of features empowers researchers to focus on innovation and scientific discovery.

OmicsBox, a leading bioinformatics tool, offers end-toend data analysis for genomes, transcriptomes and metagenomes. It also provides genetic variation studies. The application, which is used by leading private and public research institutes worldwide, allows researchers to process large and complicated data sets and streamline their analytical process. It is designed to be efficient, user-friendly and equipped with powerful tools to extract biological insight from omics data. The software is divided into modules, each of which has a set of tools and features designed to perform specific types of analyses, such as de novo genome assemblies, genetic variations analysis, differential expression analyses, taxonomic classifications, and taxonomic classes of microbiome, including the interpretation of results and rich visualizations. The functional analysis module uses the popular Blast2GO annotating methodology, making OmicsBox a great tool for non-model organisms research.

MoluCAD is a comprehensive molecular modeling and visualization application specifically designed for Windows users. This tool emerged from a three-year research initiative funded by the National Institutes of Health, which focused on developing affordable educational software tailored for chemistry students. In its most recent iteration, MoluCAD includes numerous sophisticated features typically reserved for high-end modeling software found on expensive workstations. The application is characterized by its user-friendly interface, high-quality graphics, and strong computational capabilities. Even those who are new to molecular modeling can effortlessly create models, examine them from various angles, produce animations of chemical reactions, and store all related data on their devices. Additionally, MoluCAD serves as an invaluable resource for academic institutions looking to enhance their chemistry curriculum with accessible technology.

Revolutionize the fields of drug discovery and materials research through cutting-edge molecular modeling techniques. Our computational platform, grounded in physics, combines unique solutions for predictive modeling, data analysis, and collaboration, facilitating swift navigation of chemical space. This innovative platform is employed by leading industries globally, serving both drug discovery initiatives and materials science applications across various sectors including aerospace, energy, semiconductors, and electronic displays. It drives our internal drug discovery projects, overseeing processes from target identification through hit discovery and lead optimization. Additionally, it enhances our collaborative research efforts aimed at creating groundbreaking medicines to address significant public health challenges. With a dedicated team of over 150 Ph.D. scientists, we commit substantial resources to research and development. Our contributions to the scientific community include more than 400 peer-reviewed publications that validate the efficacy of our physics-based methodologies, and we remain at the forefront of advancing computational modeling techniques. We are steadfast in our mission to innovate and expand the possibilities within our field.

Effortlessly create and share chemical structures using our online chemistry editor. Marvin Pro is a versatile drawing application that merges our advanced chemical intelligence with an intuitive interface. This tool empowers chemists, researchers, and students to quickly translate their ideas into visually appealing representations. With the capability to manage a multitude of objects, chemical structures, arrows, and text on a single canvas, Marvin Pro ensures precise alignment for all elements. Chemical editors should be user-friendly, and our solution makes it easy to visualize your chemical concepts clearly. The caliber of your drawings should reflect the dedication you invest in your research, and Marvin Pro enables you to produce high-quality visuals suitable for professional presentations. Let the canvas of Marvin Pro serve as an extension of your creativity, where you can incorporate predefined templates, color your structures, and include images from external sources. Additionally, you have the option to showcase the chemical formula alongside your structures, enhancing your visual communication even further. Whether you're drafting for a project or preparing for a presentation, Marvin Pro is designed to meet all your chemical visualization needs.

CryoTrackIMS is a comprehensive software solution tailored for various fields, including molecular biology, cell banking, cellular biology, clinical samples, biorepositories, biobanking, biochemistry, immunology, and protein laboratories, as well as high-throughput screening, quality assurance, IVF labs, and core facilities. Users can effortlessly design any box, plate, or pie layout by choosing from rows and columns or opting for a pie configuration, allowing their custom box to be generated in mere seconds for data input. Efficient inventory management of precious biological samples and specimens is essential for both fundamental research and the biotech industry. Managing extensive collections of diverse samples such as DNA, RNA, plasmids, clones, proteins, peptides, probes, antibodies, enzymes, specimens, tissues, and cell lines can often become a challenging and overwhelming endeavor that results in significant financial costs alongside frustration and wasted time. CryoTrack provides an all-encompassing solution specifically designed for laboratories within universities, clinics, biotechnology firms, and pharmaceutical organizations. This advanced software not only simplifies sample tracking but also significantly enhances lab efficiency and productivity. By streamlining the organization of critical biological materials, CryoTrackIMS empowers researchers to focus more on their experiments and less on administrative burdens.

BioNeMo is a cloud service and framework for drug discovery that leverages AI, built on NVIDIA NeMo Megatron, which enables the training and deployment of large-scale biomolecular transformer models. This service features pre-trained large language models (LLMs) and offers comprehensive support for standard file formats related to proteins, DNA, RNA, and chemistry, including data loaders for SMILES molecular structures and FASTA sequences for amino acids and nucleotides. Additionally, users can download the BioNeMo framework for use on their own systems. Among the tools provided are ESM-1 and ProtT5, both transformer-based protein language models that facilitate the generation of learned embeddings for predicting protein structures and properties. Furthermore, the BioNeMo service will include OpenFold, an advanced deep learning model designed for predicting the 3D structures of novel protein sequences, enhancing its utility for researchers in the field. This comprehensive offering positions BioNeMo as a pivotal resource in modern drug discovery efforts.

An integrated platform that bridges scientific reasoning, compound development, and computational tools is now available. Chemaxon’s Design Hub supports medicinal chemistry by facilitating the analysis and prioritization of innovative ideas. This unified platform allows users to design compounds and manage concepts seamlessly. Transitioning from traditional PowerPoint presentations to dynamic, visually engaging, and chemically searchable hypotheses enhances the compound design workflow. Users can conveniently utilize established physicochemical properties, computational models, novelty considerations, or accessible compound catalogs within an interactive visual setting. Collaborate with your Contract Research Organizations (CROs) in the compound development journey through this secure online resource. Furthermore, assess the gathered data from biological assays or experimental structural insights to derive Structure-Activity Relationships (SAR) and generate fresh hypotheses for subsequent optimization cycles. Your scientific ideas can be conveniently organized in a “designer's electronic lab notebook,” which features chemically aware drawing tools that streamline the design process. This comprehensive approach ensures that every step of compound development is efficient and well-documented, paving the way for future innovations.

The Illumina DRAGEN Secondary Analysis system offers precise, thorough, and highly efficient processing of next-generation sequencing data. Utilizing a graph reference genome alongside machine learning techniques, it achieves remarkable accuracy. The workflow is exceptionally streamlined, capable of completely analyzing a 34x whole human genome in approximately 30 minutes when using the DRAGEN server v4. Additionally, it enhances this workflow by compressing FASTQ file sizes by up to five times. This system is adept at analyzing a variety of NGS data types, including whole genomes, exomes, methylomes, and transcriptomes. It is designed to be compatible with the user's preferred platform and is scalable to meet varying requirements. DRAGEN analysis consistently ranks as a leader in accuracy for both germline and somatic variant detection, as evidenced by its performance in industry competitions conducted by precisionFDA. This advanced analysis solution empowers laboratories of all sizes and specialties to maximize the potential of their genomic datasets. Moreover, the implementation of highly adaptable field-programmable gate array (FPGA) technology allows DRAGEN to deliver hardware-accelerated genomic analysis algorithms, further enhancing its performance. Such advancements position DRAGEN as a vital tool in the ever-evolving field of genomics.

Galaxy serves as an open-source, web-based platform specifically designed for handling data-intensive research in the biomedical field. For newcomers to Galaxy, it is advisable to begin with the introductory materials or explore the available help resources. You can also opt to set up your own instance of Galaxy by following the detailed tutorial and selecting from a vast array of tools available in the tool shed. The current Galaxy instance operates on infrastructure generously supplied by the Texas Advanced Computing Center. Furthermore, additional resources are mainly accessible through the Jetstream2 cloud, facilitated by ACCESS and supported by the National Science Foundation. Users can quantify, visualize, and summarize mismatches present in deep sequencing datasets, as well as construct maximum-likelihood phylogenetic trees. This platform also supports phylogenomic and evolutionary tree construction using multiple sequences, the merging of matching reads into clusters with the TN-93 method, and the removal of sequences from a reference that are within a specified distance of a cluster. Lastly, researchers can perform maximum-likelihood estimations to ascertain gene essentiality scores, making Galaxy a powerful tool for various applications in genomic research.

All mass spectral data management and analysis can be done with one software. Quickly identify, distinguish, identify, characterize, and characterize components. ACD/MS Workbook suite is an all-in one package for MS data management. You can process MS, LC/MS and GC/MS data that you have acquired using instruments from any major vendor. Auto-annotate peaks, and associate them with compound structure. Search databases for spectral matches and deconvolute spectra to identify unknowns. Make spectral databases that are easily searchable and shareable.

Cease the struggle with cloud infrastructure and unreliable informatics tools; begin uncovering biological insights immediately. The scientific exploration process is hindered by the disjointed nature of tools utilized by biology and bioinformatics teams. To address this issue, we developed a unified bioinformatics platform that bridges the gap between wet lab and dry lab operations in the cloud, enabling teams to expedite their research and development efforts. You can easily import raw data from your cloud, your service provider, or your team's instruments with minimal hassle. Create and implement tailored bioinformatics workflows in various programming languages without the frustration of complex infrastructure management. Effortlessly execute any workflow while maintaining a comprehensive log of every analysis performed. Our platform features ready-to-use interactive visualizations for NGS data that allow you to create point-and-click plots with ease. Additionally, Latch seamlessly integrates with your organization’s AWS S3, granting access to hundreds of terabytes of data within a user-friendly organic filesystem. You can define bioinformatics workflows and dynamically generate no-code interfaces using Python, with adjustable compute and storage options to suit your needs. This innovative approach not only streamlines the research process but also fosters collaboration among teams, ultimately leading to more impactful scientific discoveries.

Combinatorial barcoding technology revolutionizes the outdated limitations of traditional single-cell methodologies. By eliminating the need for specialized instruments, it empowers researchers to make groundbreaking discoveries with ease. This innovation allows for the profiling of anywhere from 1,000 to 1 million cells or nuclei in a single experiment, driving forward unparalleled advancements in science. Evercode combinatorial barcoding technology significantly outperforms droplet-based methods, enabling researchers to increase the scale of their experiments without the constraints of previous technologies. Enjoy enhanced data quality while avoiding the complexities and requirements of outdated hardware. Conduct single-cell experiments using only a pipette and standard laboratory tools, simplifying the process and making it more accessible. The split-pool combinatorial barcoding technique facilitates scalable single-cell analysis without relying on any specialized instruments, making it easier than ever to achieve scalable sequencing. Each kit includes a comprehensive set of reagents and user-friendly analysis software, streamlining the entire workflow from start to finish for optimal efficiency. This technology not only enhances research capabilities but also fosters a new era of accessibility in scientific exploration.