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{ "count": 34450, "next": "?page=2", "previous": null, "list": [ { "name": "BRANCHSNV", "description": "BRANCHSNV reports strict clade-exclusive nucleotide markers separately from nucleotide substitutions reconstructed on a selected edge of a rooted phylogenetic tree using equal-cost Sankoff parsimony, while retaining ambiguity across globally optimal reconstructions. 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Meteor relies on genes catalogue to perform species-level taxonomic profiling (Bacteria, Archaea and Eukaryotes), functional analysis and strain-level population structure inference.", "homepage": "https://github.com/metagenopolis/meteor", "biotoolsID": "meteor", "biotoolsCURIE": "biotools:meteor", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/metagenopolis/meteor", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s40168-025-02249-w", "pmid": "41199348", "pmcid": "PMC12590682", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "vashokan", "additionDate": "2026-01-15T18:19:41.098465Z", "lastUpdate": "2026-10-06T09:07:43.353481Z", "editPermission": { "type": "group", "authors": [ "vashokan2" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SCUBA", "description": "SCUBA visually examines single cell RNA-seq data using gene co-expression networks.\nInstead of clustering cells, SCUBA groups co-expressed genes into automatically annotated modules, then shows how their activity shifts between conditions.", "homepage": "https://scuba-nw.org", "biotoolsID": "scuba-nw", "biotoolsCURIE": "biotools:scuba-nw", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_4028", "term": "Single-cell sequencing" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "Proprietary", "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://scuba-nw.org", "type": [ "Service" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "valleyofdawn", "additionDate": "2026-10-06T07:15:25.704363Z", "lastUpdate": "2026-10-06T07:16:30.381203Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioSyn Lab Calculators", "description": "Free browser-based calculators for molecular biology, biochemistry, cell culture and molecular cloning work. Twenty-plus tools cover molarity and dilution, stock and working solutions, DNA and protein molecular weight, primer melting temperature, PCR master mix setup, qPCR efficiency and delta-delta Ct, A260 and A280 concentration, plasmid molecular weight, ligation ratio, transformation efficiency, hemocytometer cell counting, trypan blue viability, seeding density, population doubling time and CFU plate counts, organised into laboratory, DNA & RNA, PCR & qPCR, cell culture, protein and molecular cloning categories. Every result page states the equation, defines each variable and walks a worked example. Each calculator is paired with a method guide explaining the formula, its assumptions and the common mistakes. All computation runs locally in the browser: no input data is uploaded, nothing is stored, and no account is required.", "homepage": "https://biosyn-inc.com/", "biotoolsID": "biosyn-lab-calculators", "biotoolsCURIE": "biotools:biosyn-lab-calculators", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Concentration and solution preparation: molarity from mass, volume or moles; C1V1 = C2V2 dilutions; stock solutions from solid or liquid; working solutions; percent w/v, v/v and w/w; ppm to mg/L.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "qPCR amplification efficiency from a standard curve by regressing Cq on log10 concentration, the -3.32 slope equivalence for 100% efficiency and the 90-110% acceptance window; population doubling time from two cell counts via t.ln2/ln(Nt/N0).", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Unit conversions across molarity, amount, mass and volume (M/mM/uM/nM, mol/mmol/umol/nmol, g/mg/ug/ng, L/mL/uL) plus ug-to-nmol, ug/mL-to-nM and mg/mL-to-uM conversions.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" }, { "uri": "http://edamontology.org/operation_3267", "term": "Sequence coordinate conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1249", "term": "Sequence length" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1249", "term": "Sequence length" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Nucleic acid and protein sizing: DNA oligo molecular weight from length or sequence using free-acid residue masses with the terminal correction and 5'-OH versus 5'-phosphate handling; plasmid molecular weight from length in bp; protein molecular weight by summing residue masses and adding one water; protein isoelectric point from ionizable groups and pKa values; GC content of a DNA or RNA sequence.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0932", "term": "Oligonucleotide probe data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Relative expression: delta-delta Ct (2^-ddCt) fold change with reference-gene normalisation, and the Livak method's efficiency and error preconditions.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1532", "term": "Protein optical density" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Spectrophotometric normalisation: nucleic acid concentration from A260 using the 50/33/40 factors with dilution-factor and path-length correction, and protein concentration from A280 with epsilon derived from Trp, Tyr and Cys content.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "Cell culture and microbiology: hemocytometer counts to cells/mL using the 1e-4 mL chamber volume and border-cell rule; trypan blue viability percentage; seeding density from target density and growth area; CFU/mL from plate counts with the 25-250 countable range.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" }, { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1249", "term": "Sequence length" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2140", "term": "Concentration" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Molecular cloning: ligation insert-to-vector molar ratio converted from fragment sizes and vector mass into nanograms of insert, and transformation efficiency in CFU per microgram with the plated-volume dilution factor applied.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" }, { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2139", "term": "Nucleic acid melting temperature" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2139", "term": "Nucleic acid melting temperature" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "PCR setup: per-reaction and total master mix volumes solved with C1V1 = C2V2, scaled by reaction count plus overage, and primer melting temperature by both the Wallace rule and the SantaLucia 1998 nearest-neighbour method.", "cmd": null } ], "toolType": [ "Web application", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0608", "term": "Cell and tissue culture" }, { "uri": "http://edamontology.org/topic_3321", "term": "Molecular genetics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [], "language": [ "JavaScript" ], "license": "Freeware", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://biosyn-inc.com/laboratory/", "type": [ "Software catalogue" ], "note": "Laboratory calculators." }, { "url": "https://biosyn-inc.com/dna-rna/", "type": [ "Software catalogue" ], "note": "DNA and RNA calculators." }, { "url": "https://biosyn-inc.com/pcr/", "type": [ "Software catalogue" ], "note": "PCR and qPCR calculators." }, { "url": "https://biosyn-inc.com/cell-culture/", "type": [ "Software catalogue" ], "note": "Cell culture calculators." }, { "url": "https://biosyn-inc.com/protein/", "type": [ "Software catalogue" ], "note": "Protein calculators." }, { "url": "https://biosyn-inc.com/cloning/", "type": [ "Software catalogue" ], "note": "Molecular cloning calculators." } ], "download": [], "documentation": [ { "url": "https://biosyn-inc.com/guides/what-is-molarity/", "type": [ "User manual" ], "note": "What molarity means: moles per litre, M vs mM, and why temperature changes the answer." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-molarity/", "type": [ "User manual" ], "note": "Molarity in three steps with worked examples for NaCl, glucose and a 10 mM reagent." }, { "url": "https://biosyn-inc.com/guides/c1v1-equation/", "type": [ "User manual" ], "note": "C1V1 = C2V2 explained: all four rearrangements, the unit-matching rule, and 10x stock mapping." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-a-dilution/", "type": [ "User manual" ], "note": "Find stock volume, diluent volume, dilution factor or final concentration, with ratio and percentage tables." }, { "url": "https://biosyn-inc.com/guides/how-to-make-a-serial-dilution/", "type": [ "User manual" ], "note": "Plan a serial dilution: tube-by-tube concentrations, transfer and diluent volumes, pipetting errors." }, { "url": "https://biosyn-inc.com/guides/how-to-make-a-stock-solution/", "type": [ "User manual" ], "note": "Mass = MW x M x V, the 80% rule, hydrate and purity corrections, per-compound recipes." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-dna-molecular-weight/", "type": [ "User manual" ], "note": "Free-acid residue masses, terminal correction, 5'-OH vs 5'-phosphate, ug-to-nmol." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-dna-concentration/", "type": [ "User manual" ], "note": "A260 to concentration: the 50/33/40 factors, dilution factor, path length, ug/mL to nM." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-gc-content/", "type": [ "User manual" ], "note": "GC% = (G + C) / length x 100 with IUPAC degenerate-base rules." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-primer-tm/", "type": [ "User manual" ], "note": "Wallace rule and SantaLucia 1998 nearest-neighbour method with a worked example." }, { "url": "https://biosyn-inc.com/guides/how-to-choose-annealing-temperature/", "type": [ "User manual" ], "note": "Tm-5 empirical start, Rychlik Ta-optimum formula, gradient windows, mismatched primers." }, { "url": "https://biosyn-inc.com/guides/how-to-make-a-pcr-master-mix/", "type": [ "User manual" ], "note": "Solve each component with C1V1=C2V2, scale by reactions plus overage, balance the water." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-qpcr-efficiency/", "type": [ "User manual" ], "note": "Regress Cq on log10 concentration, why slope -3.32 is 100%, the 90-110% window." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-delta-delta-ct/", "type": [ "User manual" ], "note": "Livak 2^-ddCt by hand: normalise to a reference gene, subtract control, check efficiency first." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-protein-molecular-weight/", "type": [ "User manual" ], "note": "Sum residue masses and add one water; average vs monoisotopic; sources." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-protein-isoelectric-point/", "type": [ "User manual" ], "note": "Ionizable groups, pKa values, the net-charge sum and why iteration is required." }, { "url": "https://biosyn-inc.com/guides/how-to-determine-protein-concentration-a280/", "type": [ "User manual" ], "note": "Derive epsilon280 from Trp/Tyr/Cys, apply Beer-Lambert, convert to mg/mL and uM." }, { "url": "https://biosyn-inc.com/guides/how-to-count-cells-with-hemocytometer/", "type": [ "User manual" ], "note": "The 1e-4 mL chamber volume, why you multiply by 10^4, the border-cell rule." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-cell-viability/", "type": [ "User manual" ], "note": "Trypan blue counts: viability % = live/total x 100, viable density, the ~90% threshold." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-seeding-density/", "type": [ "User manual" ], "note": "Target density to cells per well, growth-area conversion, C1V1=C2V2 for the stock volume." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-doubling-time/", "type": [ "User manual" ], "note": "Td = t.ln2/ln(Nt/N0), the log2 form, specific growth rate, PDL vs passage number." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-cfu/", "type": [ "User manual" ], "note": "CFU/mL from colony counts: dilution factor, plated volume, the 25-250 countable range." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-plasmid-molecular-weight/", "type": [ "User manual" ], "note": "660 g/mol.bp convention, then pmol/ug, molarity, molecules and copy number." }, { "url": "https://biosyn-inc.com/guides/how-to-calculate-ligation-ratio/", "type": [ "User manual" ], "note": "Insert:vector molar ratio from fragment sizes 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