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@seosiri/biopharma-mcp

SEOSiri Biopharma MCP Server on Glama

📖 Official Architecture & Documentation: SEOSiri Biopharma Technical Guide | Developer Portal & Graph Explorer | Central MCP Directory

An open-source, local-first Model Context Protocol (MCP) server written in TypeScript for Biopharma Software Infrastructure, FDA 21 CFR Part 11 GxP Audit Trailing, CDISC SDTM/Allotrope Data Exports, 4PL Dose-Response Curve Fitting, and HIPAA PII/PHI Redaction.


🛡️ Enterprise Compliance & Regulatory Clauses

1. FDA 21 CFR Part 11 Audit Trail Clause

All operational tool executions generate an immutable SHA-256 cryptographic digest written directly to the stderr stream (generate_gxp_audit_log). This preserves audit trail integrity, operator identification, and timestamp sequence rules without altering the standard JSON-RPC data payload.

2. HIPAA PII/PHI Privacy Redaction Clause

Every data payload passed through memory is automatically processed by a zero-latency privacy cleaning loop (redactPatientPii). Common sensitive patient identifiers—including Social Security Numbers (SSN), email addresses, Date of Birth (DOB) strings, and telephone patterns—are redacted prior to memory serialization or cloud database pooling.

3. Data-at-Rest AES-256-GCM Encryption Clause

Database connection parameters and sensitive data fields stored in cloud instances are encrypted using AES-256-GCM blocks with random 12-byte initialization vectors (IVs) and authentication tags (encryptRestData / decryptRestData).


Related MCP server: MCP Healthcare Server

🚀 10 Zod-Validated Production Tools

  1. calculate_4pl_curve: Fits 4-Parameter Logistic non-linear regression sigmoidal dose-response curves.

  2. assess_parallelism: Computes shared slope and asymptotes consistency via F-Test and TOST equivalence metrics.

  3. calculate_z_factor: Validates microplate high-throughput screening (HTS) quality from positive and negative control series.

  4. parse_large_plate_stream: Memory-safe stream parser for 96-well or 384-well microplate layout string rows.

  5. resolve_biological_entity_safe: Fault-tolerant Circuit Breaker container for ChEBI and PubChem compound queries.

  6. detect_assay_outliers: Grubbs and IQR mathematical filtering boundaries to detect and drop anomalous microplate artifacts.

  7. calculate_lod_loq: Calculates Limit of Detection (LOD) and Limit of Quantitation (LOQ) from background blank deviations.

  8. normalize_dilution_potency: Scales observed target calculations dynamically across complex serial dilution ratios.

  9. export_cdisc_sdtm: Converts internal JSON records into CDISC SDTM v1.7 / Allotrope Data Model compliant structural models.

  10. generate_gxp_audit_log: Records immutably hashed operation logs to maintain compliance with FDA 21 CFR Part 11.


📦 Installation & Setup Guide

1. Install via NPM / NPX

# Global installation
npm install -g @seosiri/biopharma-mcp

# Local project installation
npm install @seosiri/biopharma-mcp

2. Build and Test Locally

# Compile TypeScript to ESM (dist/index.js)
npm run build

# Run unit test suite
npm test

🔌 AI Host Client Integrations

Claude Desktop Setup

Add this to your claude_desktop_config.json file:

{
  "mcpServers": {
    "seosiri-biopharma": {
      "command": "node",
      "args": [
        "D:/biopharma-mcp/dist/index.js"
      ]
    }
  }
}

Cursor IDE Setup

Add this to your mcp.json file or configure it directly in the IDE settings:

{
  "mcpServers": {
    "seosiri-biopharma": {
      "command": "npx",
      "args": [
        "-y",
        "@seosiri/biopharma-mcp"
      ]
    }
  }
}

💖 Sponsorship, B2B Custom Solutions & Attribution

Lead Architect

Designed and engineered by Momenul Ahmad, Lead Architect and Founder of SEOSiri.

Enterprise B2B Custom Development

SEOSiri provides high-ticket systems architecture, custom biopharma MCP tool engineering, and Cloudflare Zero Trust gateway integration for corporate clients in the United States, United Kingdom, Canada, Germany, and Japan.

💼 Commercial Licensing & High-Throughput API Keys

Need more than 30 requests/minute for production?

  • Free Tier: 30 req/min (Default, public).

  • Pro Tier ($299/mo): 1,000 req/min across all edge gateways with signed API key.

  • Enterprise ($2,500): Dedicated Cloudflare Zero Trust VPC, custom MCP tools, and SLA support.

  • Payment Method: Payoneer (badhan_pbn@yahoo.com) or direct wire.

  • Developer Portal: developers.seosiri.com | Contact Desk: info@seosiri.com

License

Distributed under the MIT License.

Available Tools

10 tools
assess_parallelismB

Computes shared slope and asymptotes consistency via F-Test and TOST metrics.

ParametersJSON Schema
NameRequiredDescriptionDefault
test_responsesYes
reference_responsesYes

TDQS

B3.1/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries full responsibility for disclosing behavior. While it names the statistical tests, it fails to describe output format, assumptions, or whether it returns a decision/p-value. It does not mention any side effects, auth needs, or data constraints, making behavioral expectations unclear.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, well-structured sentence with no redundant words. It conveys the essential method succinctly, making it easy for an agent to parse.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's complexity (statistical testing) and the absence of output schema and annotations, the description is incomplete. It does not describe what the tool returns (e.g., a statistic, p-value, or decision), nor does it mention required input assumptions or edge cases. Without this, an agent cannot fully predict the tool's behavior after invocation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, and the description adds no meaning to the parameters. It does not explain what 'reference_responses' and 'test_responses' represent or how they relate to the slope/asymptote analysis. The parameter names are somewhat self-explanatory, but the description fails to compensate for the lack of schema documentation.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's function with a specific verb ('Computes') and identifiable resource ('shared slope and asymptotes consistency'), specifying the statistical methods (F-Test and TOST). This distinguishes it from sibling tools like calculate_4pl_curve or calculate_z_factor, which address different aspects of assay analysis.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No information is provided about when to use this tool versus alternatives, prerequisites, or data preparation. It does not compare itself to sibling tools or mention any exclusions, leaving the agent without guidance on selecting it over related statistical tools.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

calculate_4pl_curveC

Fits and resolves 4-Parameter Logistic non-linear regression sigmoidal dose-response fields.

ParametersJSON Schema
NameRequiredDescriptionDefault
responsesYes
concentrationsYes

TDQS

C2.6/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden of behavioral disclosure. It does not state whether the operation is read-only, what side effects (if any) occur, what the return format is, or whether there are computational constraints. This is a significant gap for a complex regression tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single concise sentence with no filler. Every word contributes to the topic, though the phrase 'resolves... fields' is slightly awkward and could be clearer. It is appropriately short for the information it conveys.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness1/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

This tool is complex (non-linear regression) with no output schema and no annotations. The description provides no information about expected output, input validation, error conditions, or typical use cases. An agent would need more context to invoke this correctly, such as knowing that it returns curve parameters and requires paired arrays.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, and the description does not mention the parameters (concentrations, responses) or clarify their roles. The parameter names are somewhat self-explanatory, and the mention of 'dose-response' hints at their relationship, but the description fails to compensate for the lack of schema descriptions or specify required pairings or constraints.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description identifies a specific analysis task (4PL non-linear regression) and names the resource ('sigmoidal dose-response fields'). However, the phrase 'resolves... fields' is imprecise and does not clarify whether it returns fitted parameters, goodness-of-fit, or a curve object. It does not differentiate from sibling tools like calculate_z_factor or calculate_lod_loq.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance is provided about when to use this tool versus alternatives. The description does not mention any prerequisites (e.g., matching array lengths, positive concentrations) or exclusions. It simply defines what the tool does without contextualizing its use.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

calculate_lod_loqC

Calculates Limit of Detection (LOD) and Limit of Quantitation (LOQ) from background blanks.

ParametersJSON Schema
NameRequiredDescriptionDefault
slopeYes
blank_responsesYes

TDQS

C2.9/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are present, so the description carries full responsibility. It only states the calculation but does not disclose the formula, return format, or any assumptions about the blank responses (e.g., normality, sufficient count). This leaves a significant gap in behavioral expectations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single sentence, concise and front-loaded. However, it is almost tautological with the tool name, providing minimal additional value beyond what the name already conveys.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a 2-parameter calculation tool with no output schema, the description is too thin to fully prepare an agent. It does not mention what is returned (e.g., a tuple of LOD and LOQ) or any constraints on input data length. The sibling tools suggest a domain context where such details matter.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, and the description does not explain the meaning of 'slope' or the expected structure of 'blank_responses.' While the parameter names are suggestive, the description adds no semantic detail beyond the schema's bare types.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Calculates') and clearly identifies the resource ('Limit of Detection (LOD) and Limit of Quantitation (LOQ)') and the input source ('background blanks'), which distinguishes it from sibling tools like calculate_4pl_curve or calculate_z_factor.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool versus alternatives, such as assess_parallelism or detect_assay_outliers. No context, prerequisites, or exclusions are mentioned.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

calculate_z_factorC

Validates microplate HTS metrics from positive and negative control data series.

ParametersJSON Schema
NameRequiredDescriptionDefault
negative_controlsYes
positive_controlsYes

TDQS

C2.4/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden of explaining behavior. It states that the tool 'validates' metrics, but does not disclose what validation involves, whether a Z-factor value is returned, how edge cases are handled, or what errors might occur. This is too vague for an agent to predict the tool's actual behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, efficient sentence with no filler. It is front-loaded with the key concept of validation, though this comes at the cost of specificity. It is appropriately sized for a short description, but could be slightly expanded to include the actual output metric without losing conciseness.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With no annotations, no output schema, and two unannotated parameters, the description leaves significant gaps. It does not state the return value (presumably the Z-factor), how success is measured, or any details about the calculation context. In the presence of related sibling tools, this description is insufficient for an agent to invoke the tool correctly and interpret its result.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema lists two array parameters without descriptions, giving 0% schema coverage. The description adds only that positive and negative controls are involved, but does not explain what the values represent, expected array lengths, units, or how the arrays are used in the calculation. This minimal information does not sufficiently compensate for the missing schema documentation.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description says 'Validates microplate HTS metrics' but does not specifically mention calculating the Z-factor, which is the tool's clear purpose implied by its name. The verb 'validates' is ambiguous and does not distinguish this tool from siblings like assess_parallelism or detect_assay_outliers. A more precise description such as 'calculates the Z-factor from positive and negative control measurements' would be clearer.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no guidance on when to use this tool versus alternatives. The description only indicates that it operates on positive and negative controls, but does not state the broader context (e.g., assay quality assessment) or compare against sibling tools. No exclusions or prerequisites are mentioned.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

detect_assay_outliersC

Employs Grubbs and IQR mathematical boundaries to filter anomalous microplate artifacts.

ParametersJSON Schema
NameRequiredDescriptionDefault
methodNo
replicate_valuesYes

TDQS

C2.4/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description must fully disclose behavioral traits, but it only states the mathematical boundaries used (Grubbs and IQR). It does not clarify whether outliers are removed, flagged, or returned separately, nor does it mention edge cases like missing values or empty arrays. For a filtering operation, this lack of detail is a significant gap.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise (one sentence) and front-loaded with the methods. However, it is under-specification rather than genuine conciseness: it omits critical operational details that would be necessary for correct use, so it does not earn its place as a complete summary.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given no output schema, no annotations, and sparse parameter documentation, the description is incomplete. It lacks information on what the function returns (e.g., outlier indices, filtered data), how the method affects behavior, and any expected data format or constraints. The moderate complexity of the tool demands more detail.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It mentions Grubbs and IQR but does not explain the purpose of 'replicate_values' (the only required parameter) or how the 'method' parameter selects between the two boundaries. The description adds no semantic meaning beyond what the schema already shows.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('filter') and names the resource ('anomalous microplate artifacts'), so the core action is clear. It also distinguishes the tool from generic 'detect' tools by mentioning the methods (Grubbs and IQR), giving some specificity. However, it could be more explicit that this is an outlier detection tool, as 'filter' might imply removal rather than flagging.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance is given on when to use this tool versus alternatives. The sibling tools like calculate_4pl_curve or assess_parallelism suggest overlapping assay analysis contexts, but the description does not mention any conditions, prerequisites, or scenarios where this tool is preferred.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

export_cdisc_sdtmC

Converts unstructured JSON payload records into CDISC SDTM / Allotrope compliant models.

ParametersJSON Schema
NameRequiredDescriptionDefault
study_idYes
test_codeYes
subject_idYes
result_unitYes
numeric_resultYes

TDQS

C2.4/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations available, the description carries the full burden of behavioral disclosure. It only states the conversion action without disclosing side effects, error handling, input validation, whether the operation is read-only or mutating, or any output format details. This insufficient disclosure merits a 2.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single sentence with no redundant words, making it highly concise and front-loaded. However, the brevity results in under-specification, so it earns a 4 for conciseness but not a 5.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness1/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool converts data between formats, a process that likely involves validation, transformation rules, and error conditions. Without an output schema or annotations, the description fails to explain the output structure, failure modes, or prerequisites, making it contextually incomplete for a tool with this complexity.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema lists five required parameters with no descriptions. The tool description provides no additional semantics for these parameters, leaving the agent to infer their meaning from names alone. With schema description coverage at 0%, the description completely fails to compensate, making this a 1.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's function: converting unstructured JSON payload records into CDISC SDTM/Allotrope compliant models. This provides a specific verb and resource, and it's distinct from sibling tools which are analytical calculations. However, it doesn't explicitly differentiate from siblings or mention related tools, so it falls short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance is provided on when to use this tool versus alternatives, nor any prerequisites, exclusions, or context. The description lacks any instruction on when this conversion should be performed, leaving the agent without usage direction.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

generate_gxp_audit_logA

Records immutably hashed operation logs to maintain compliance with FDA 21 CFR Part 11.

ParametersJSON Schema
NameRequiredDescriptionDefault
operator_idYes
resource_targetYes
action_performedYes

TDQS

A3.5/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description must carry the behavioral transparency burden. It discloses immutability and hashing, which are important traits, but omits permissions, error handling, return value, and persistence details.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, well-structured sentence that communicates the core action, key behavioral attribute (immutable hashing), and purpose. No wasted words.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite a clear purpose, the tool has no annotations, no output schema, and three undocumented parameters. The description lacks usage context, parameter details, and return/error behavior, which are critical for a tool that performs a write-like operation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0% and the description provides no explanation of operator_id, action_performed, or resource_target. The parameter names are somewhat self-explanatory, but the description does not add meaning about formats, constraints, or relationships.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Records') and resource ('operation logs'), and clearly states the regulatory purpose. It distinguishes itself from sibling analytical/processing tools by focusing on audit log generation.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies use for FDA 21 CFR Part 11 compliance, but does not explicitly state when to use this tool versus alternatives or any exclusions. The sibling tools are in different domains, so no direct differentiation is provided.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

normalize_dilution_potencyC

Scales observed calculations dynamically across dilution ratios back to original stock concentration.

ParametersJSON Schema
NameRequiredDescriptionDefault
dilution_factorYes
observed_concentrationYes

TDQS

C2.7/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden of behavioral disclosure. It mentions the scaling action but doesn't disclose edge cases (e.g., zero dilution factor), units, or whether the operation is safe read-only or mutating. It also doesn't describe the return value or error behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, compact sentence with no redundant words. It is front-loaded with the key action. However, it is almost too terse, sacrificing clarity for brevity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the simple two-parameter tool and absence of output schema or annotations, the description covers the core purpose but lacks details on the exact calculation, parameter definitions, and output. An agent would need to infer the formula and units, which is risky. The tool appears part of a larger assay analysis suite, but no contextual connection is provided.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It hints that observed_concentration is the diluted measurement and dilution_factor is the ratio, but it doesn't explicitly name the parameters or provide the formula. This is minimal semantic addition and may leave the agent uncertain about exact units or input formats.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('scales') and states the resource ('observed calculations ... back to original stock concentration'). It distinguishes from sibling tools which focus on curve fitting, parallelism, z-factor, etc. However, 'observed calculations' is somewhat vague and the plural 'dilution ratios' doesn't align perfectly with the singular 'dilution_factor' parameter.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No explicit guidance on when to use this tool versus alternatives. The description implies use for normalization of dilution-related measurements but doesn't state exclusions, prerequisites, or context such as assay types. Sibling tools are not referenced.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

parse_large_plate_streamC

Memory-safe stream parser for 96-well or 384-well microplate layout string rows.

ParametersJSON Schema
NameRequiredDescriptionDefault
format_wellsNo
plate_layout_csvYes

TDQS

C2.9/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of disclosing behavior. It mentions 'memory-safe stream' which hints at memory-efficient processing, but it does not disclose return format, validation behavior, error handling, or side effects. This is insufficient for a tool with no annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is one sentence, front-loaded with the key action ('parser') and resource. Every word contributes meaning ('memory-safe', 'stream', '96-well or 384-well'), with no redundant or verbose language.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the absence of annotations and output schema, the description should provide a complete picture of what the tool does, how to use it, and what it returns. It lacks essential details such as input format specifics, output structure, and parameter explanation, making it inadequate for a complex parser tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, and the description does not explain the parameters at all. It does not describe the expected format of 'plate_layout_csv' or how 'format_wells' affects parsing. The description adds no value beyond the raw schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly identifies the tool as a parser for 96-well or 384-well microplate layout string rows. It uses a specific verb ('parser') and defines the exact resource and format scope. This clearly distinguishes it from the analysis-focused sibling tools.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for large plate layouts via 'memory-safe stream', but it does not provide explicit when-to-use guidance, prerequisites, or alternatives. No mention of whether this should be used before analysis tools or when the input size warrants streaming.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

resolve_biological_entity_safeB

Fault-tolerant Circuit Breaker query for ChEBI or PubChem compound resolution.

ParametersJSON Schema
NameRequiredDescriptionDefault
compound_nameYes
target_databaseNo

TDQS

B3.1/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of behavioral disclosure. It does disclose two behavioral traits: fault tolerance and circuit breaker behavior, which signal that the tool is designed to handle failures gracefully. However, it lacks specifics on what happens upon failure (e.g., returns null, throws, or falls back), and it does not describe the return format or any side effects. The disclosure is present but minimal.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, front-loaded sentence that immediately states the tool's nature and purpose. It is concise and easy to parse, with no wasted words. It earns a high score for brevity, though it sacrifices some detail that could have been included without becoming verbose.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the absence of annotations and an output schema, the description should provide more context about expected inputs, outputs, and failure behavior. The tool has a simple schema, but the description is too terse to be self-sufficient. It does not explain what 'safe' means in practice, nor what the user should expect as a return value. This leaves significant gaps for an agent trying to invoke the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema coverage is 0%, so the description must compensate. It indirectly explains target_database by naming ChEBI and PubChem, which aligns with the enum values. For compound_name, the phrase 'compound resolution' implies it is the compound to be resolved. This adds some semantic context beyond the raw schema, but the description does not explicitly name or explain either parameter, leaving ambiguity about input formats or acceptable values.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly identifies the tool as a query for compound resolution against ChEBI or PubChem, using the specific verb 'query' and naming the target resources. It distinguishes itself from sibling tools, which are all about assay calculations and statistics, by focusing on biological entity resolution. However, it could be more explicit about what 'resolution' entails (e.g., mapping names to IDs), so it is not a full 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no explicit guidance on when to use this tool versus alternatives. It mentions 'Fault-tolerant Circuit Breaker' in the description, which hints at use cases requiring resilience, but it does not state clear conditions, prerequisites, or exclusions. Sibling tools are thematically unrelated, but no alternatives or counter-indications are given.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. 10 tool updatesv1.0.0
    • First observedassess_parallelism
    • First observedcalculate_4pl_curve
    • First observedcalculate_lod_loq
    • First observedcalculate_z_factor
    • First observeddetect_assay_outliers
    • First observedexport_cdisc_sdtm
    • First observedgenerate_gxp_audit_log
    • First observednormalize_dilution_potency
    • First observedparse_large_plate_stream
    • First observedresolve_biological_entity_safe

TDQS

B3.3/5.0
Disambiguation5/5

Each tool targets a distinct function: curve fitting, parallelism assessment, Z-factor calculation, plate parsing, entity resolution, outlier detection, LOD/LOQ, dilution normalization, data export, and audit logging. No two tools overlap in purpose, and descriptions clarify their unique roles.

Naming Consistency5/5

All tool names follow a consistent verb_noun pattern in snake_case, such as calculate_4pl_curve, parse_large_plate_stream, and generate_gxp_audit_log. The naming is uniform and predictable, making it easy to infer tool behavior.

Tool Count5/5

The server contains 10 tools, which is within the ideal 3-15 range for a well-scoped domain. Each tool covers a distinct aspect of biopharma data analysis and compliance without redundancy or bloat.

Completeness4/5

The tool surface covers the primary assay analysis workflow: input parsing, entity resolution, statistical analysis (curve fitting, parallelism, Z-factor, outliers, LOD/LOQ), normalization, and output/export with audit logging. Minor gaps exist, such as the absence of direct IC50 extraction or data visualization tools, but these are not critical to core functionality.

Maintenance

ActivityMaintained
ResponsivenessNo issues

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