Information

Difference between modules in KEGG Module


The KEGG module M00115 includes a set of reactions while M00542 does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?


Module means, as defined in the KEGG Module page, a functional unit. So it can be anything, from groups of enzymes to genes to metabolites. About the two that concerns you:

  • Pathway modules represent groups of functionally related enzymes part of the metabolic network. I think this one is easy to understand because it represents the classical understanding of "module". The modules involve metabolites (compounds with id starting with "C"), enzymes (represented by KEGG ortholog ids starting with "K") and reactions (represented by ids starting with "R"). The reactions integrate compounds and enzymes in a particular step in the chain of reactions included in that module.

  • Signature modules represent molecules associated with a particular phenotype. In particular, the example listed in the KEGG page points to EHEC pathogenicity signature, Shiga toxin. The two molecules in module M00363 are associated with the phenotype, which is in this case EHEC pathogenicity. But in principle they do not necessarily need to be related to each other (in this case they are, but not in the same meaning as the metabolic module).

In your particular examples, M00115 is again a pathway module including enzymes, compounds and reactions, all connected in an integrated manner. Module M00542 on the other hand shows the proteins part of the T3SS (Type three secretion system) used by Gram-negative bacteria for infection. These are not enzymatic reactions, just proteins associated with the EHEC/EPEC pathogenicity phenotype. They are however related in that they form a protein interaction complex that mediates infection.

Other Module categories include:

  • Structure complexes related to molecular machineries.
  • Functional sets seems like a miscellaneous category.

You could argue that the T3SS is a molecular machine and should be classified in the Structural complexes category. Indeed, something important to remember is, as stated in the KEGG module's page:

KEGG MODULE is a collection of manually defined functional units [… ]

As anything manually defined, there is some degree of arbitrariness. Use the information in KEGG modules as far as it serves your needs, but it would be better not take it as written in stone.


M00115 is a pathway module (NAD biosynthesis) whereas M00542 is a signature module (EHEC/EPEC pathogenicity signature).

From the KEGG page on modules:

  • pathway modules - representing tight functional units in KEGG metabolic pathway maps, such as M00002 (Glycolysis, core module involving three-carbon compounds)

  • signature modules - as markers of phenotypes, such as M00363 (EHEC pathogenicity signature, Shiga toxin)


Modularity

Broadly speaking, modularity is the degree to which a system's components may be separated and recombined, often with the benefit of flexibility and variety in use. [1] The concept of modularity is used primarily to reduce complexity by breaking a system into varying degrees of interdependence and independence across and "hide the complexity of each part behind an abstraction and interface". [2] However, the concept of modularity can be extended to multiple disciplines, each with their own nuances. Despite these nuances, consistent themes concerning modular systems can be identified. [3]


Types of Canal Outlets (With Design and Diagram)

Canal outlets are of the following three types: 1. Non-Modular Outlets 2. Semi-Modular Outlets 3. Modular Outlets.

Type # 1. Non-Modular Outlets:

In non-modular canal outlets, discharge capacity depends on the difference of water levels in the distributary and the watercourse. The discharge through non- modular outlets fluctuates over a wide range with variations in the water levels of either the distributary or the watercourse. The non-modular canal outlet is controlled by a shutter at its upstream end. Loss of head in non-modular outlet is less than that in a modular outlet.

Hence, non-modular canal outlets are very suitable for low head conditions. However, in non-modular canal outlets, the dis­charge may vary even when the water level in the distributary remains constant. Hence, it is very difficult to ensure equitable distribution of water at all outlets at times of keen demand of water.

The non-modular canal outlet is usually in the form of a submerged pipe outlet or a masonry sluice which is fixed in the canal bank at right angle to the direction of flow in the distributary. The diameter of the pipe varies from 10 to 30 cm. The pipe is laid on a light concrete foundation to avoid uneven settlement of the pipe and consequent leakage problems.

The pipe inlet is generally kept about 25 cm below the water level in the distributary. When considerable fluctuation in the distributary water level is anticipated, the inlet is so fixed that it is below the minimum water level in the distributary. Figure 7.9 shows a pipe outlet.

Obviously, the discharge through non-modular outlets varies with water levels in the distributary and the watercourse. In case of fields located at high elevations, the watercourse level is high and, hence, the discharge is relatively small. But in case of fields located at low elevations, the discharge is relatively larger due to lower water course levels.

Further, depending upon the amount of withdrawal of water in the head reaches, the tail reach may be completely dry or get flooded. The discharge through pipe outlets can be increased by deepening the watercourse and thereby lowering the water level in it. The discharge varies from outlet to outlet because of flow conditions and also at different times on the same outlet due to sediment discharge in the dis­tributary channel.

As such, proper and equitable distribution of water is very difficult. These are serious drawbacks of pipe outlets. The non-modular outlets can, however, work well for low heads too and this is their chief merit. Pipe outlets are adopted in the initial stages of distribution or for additional irrigation in a season when excess supply is available.

Type # 2. Semi-Modular Outlets:

The discharge through a semi-modular canal outlet (or semi-module or flexible outlet) depends only on the water level in the distributary, and is unaffected by the water level in the watercourse provided a minimum working head required for its working is available.

A semi-module is more suitable for achieving equitable distribution of water at all outlets of a distributary. The only disad­vantage of a semi-modular canal outlet is that it involves comparatively greater loss of head.

The simplest type of semi-modular canal outlet is a pipe outlet discharging freely into the atmosphere. The pipe outlet described as non-modular outlet works as semi-module when it discharges freely into the watercourse. The exit end of the pipe is placed higher than the water level in the watercourse.

In this case, working head H is the difference between water level in the distributary and the centre of the pipe outlet. The discharge through the pipe outlet cannot be increased by the cultivator by digging the watercourse and, thus, lowering the water level of the watercourse. Other types of flexible outlets include Kennedy’s gauge outlet, open flume outlet and orifice semi-modules.

(i) Kennedy’s Gauge Outlet:

This outlet was developed by R.G. Kennedy in 1906. It mainly consists of an orifice with bellmouth entry, a long-expanding delivery pipe and an interven­ing vertical air column above the throat (Fig. 7.10). The air vent pipe permits free circulation of air around the jet.

This arrangement makes the discharge through the outlet independent of the water level in the watercourse. The water jet enters the cast iron expanding pipe which is about 3 m long and at the end of which a cement concrete pipe extension is generally provided. Water is then discharged to the watercourse.

This outlet can be easily tampered with by the cultivator who blocks the air vent pipe to increase the discharge through the outlet. Because of this drawback and its high cost, Kennedy’s gauge outlet is generally not used.

An open flume outlet is a weir with sufficiently constricted throat to ensure supercritical flow, and long enough to ensure that the controlling section remains within the throat at all discharges up to the maximum. A gradual expansion is provided downstream of the throat. The entire structure is built in brick masonry, but the controlling section is generally provided with cast iron or steel bed and check plates.

This arrangement ensures the formation of hydraulic jump and hence the outlet discharge remains independent of the water level in the watercourse. Figure 7.11 shows an open flume outlet which is commonly used in Punjab. The discharge through the canal outlet is proportional to H 3/2 .

(iii) Orifice Semi-Modules:

An orifice semi-module consists of an orifice followed by a gradually expand­ing flume on the downstream side (Fig. 7.12). Supercritical flow through the orifice causes the formation of hydraulic jump in the expanding flume and, hence, the outlet discharge remains independent of the water level in the watercourse.

The roof block is suitably shaped to ensure converging stream­lines so that the discharge coefficient does not very much. The roof block is fixed in its place by means of two bolts which are embedded in a masonry key. For adjustment, this masonry can be dismantled and the roof block is suitably adjusted.

After this, the masonry key is rebuilt. Thus, the adjustment can be made at a small cost. However, tampering with the outlet by the cultivators would be easily noticed through the damage to the masonry key. This is the chief merit of this outlet.

Type # 3. Modular Outlets:

In modular canal outlets, the discharge is independent of the water levels in the distributary and the watercourse, within reasonable working limits. These outlets may have moving parts or may be without moving parts. In the latter case, these are called rigid modules. The modular canal outlets with moving parts are not simple to design and construct and are, hence, expensive.

A modular canal outlet supplies fixed discharge and, therefore, enables the farmer to plan his irrigation accordingly. However, in case of excess or deficient supplies in the distributary, the tail-end reach of the distributary may either get flooded or be deprived of water. This is due to the reason that the modular outlet would not adjust its discharge according to the level in the distributary.

But, if an outlet is to be provided in a branch canal which is likely to run with large fluctuations in discharge, a modular outlet would be an ideal choice. The outlet would be set at a level low enough to permit it to draw its due share when the branch is running with low supplies.

When the branch has to carry excess supplies to meet the demands of the distributaries, the discharge through the modular outlet would not be affected, and the excess supplies would reach up to the desired distributaries.

Similarly, if an outlet is desired to be located upstream of a regulator or a raised crest fall, a modular outlet would be a suitable choice. Most of the modular outlets have moving parts which make them costly to install as well as maintain.

Following two types of modular outlets (also known as rigid modules), however, do not have any moving part:

This module has an inlet pipe under the distributary bank. This pipe takes water from distributary to a rising spiral pipe which joins the eddy chamber (Fig. 7.13). This arrangement results in free vortex motion. Due to this free vortex motion, there is heading up of water (due to smaller velocity at larger radius—a characteristic of vortex motion) near the outer wall of the rising pipe. The water surface, thus, slopes towards the inner wall.

A number of baffle plates of suitable size are suspended from the roof of the eddy chamber such that the lower ends of these plates slope against the flow direction.

With the increase in head, the wafer bank up at the outer wall of the eddy chamber and impinges against the baffles and spins round in the compartment between two successive baffle plates. This causes dissipation of excess energy and results in constant discharge. The outlet is relatively more costly and its sediment withdrawal is also not good.

(ii) Khanna’s Rigid Orifice Module:

This canal outlet is similar to an orifice semi-module. But it has, in addition, sloping shoots fixed in the roof block (Fig. 7.14). These shoots cause back flow and, thus, keep the outlet discharge constant.

If the water level in the distributary is at or below its normal level, the outlet behaves like an orifice semi-module. But when the water level in the parent channel is above its normal level, water level rises in chamber A and enters the first sloping shoot. This causes back flow and dissipates additional energy.

This results in maintaining a constant discharge. The number of sloping shoots and their height above the normal level can vary to suit local requirements. The shoots are housed in a chamber so that these cannot be tampered with. If the shoots are blocked, the outlet continues to function as a semi-module.


4 Answers 4

The terms are similar. I generally think of a "module" as being larger than a "component". A component is a single part, usually relatively small in scope, possibly general-purpose. Examples include UI controls and "background components" such as timers, threading assistants etc. A "module" is a larger piece of the whole, usually something that performs a complex primary function without outside interference. It could be the class library of an application that provides integration with e-mail or the database. It may be as large as a single application of a suite, such as the "Accounts Receivable module" of an ERP/accounting platform.

I also think of "modules" as being more interchangeable. Components can be replicated, with new ones looking like old ones but being "better" in some way, but typically the design of the system is more strictly dependent upon a component (or a replacement designed to conform to that component's very specific behavior). In non-computer terms, a "component" may be the engine block of a car you can tinker within the engine, even replace it entirely, but the car must have an engine, and it must conform to very rigid specifications such as dimensions, weight, mounting points, etc in order to replace the "stock" engine which the car was originally designed to have. A "module", on the other hand, implies "plug-in"-type functionality whatever that module is, it can be communicated with in such a lightweight way that the module can be removed and/or replaced with minimal effect on other parts of the system. The electrical system of a house is highly modular you can plug anything with a 120V15A plug into any 120V15A receptacle and expect the thing you're plugging in to work. The house wiring couldn't care less what's plugged in where, provided the power demands in any single branch of the system don't exceed safe limits.


Sample level enrichment analysis and KEGG pathway module

The sample level enrichment analysis (SLEA) is a novel methodology that has a more general use for enrichment analysis at the level of individual samples and is widely accepted recently [11-17]. The pathways or modules are represented as lists of genes, which can be obtained from the literature or online repositories such as Gene Ontology and KEGG, as well as determined through other high-throughput assays. Without using a priori phenotypic information about the samples, the SLEA calculates an enrichment score per sample per gene set using the z-test. This score is used to determine the relative importance of the corresponding module or pathway in different patient groups [11, 13].

In this study, the enrichment analysis for each sample was performed using Gitools version 1.6.0. We used the z-score method as described above. This method compares the mean (or median) expression value of genes in each module to a distribution of mean (or median) of 10, 000 random modules of the same size drawn from the expression values for the same sample. The result of this enrichment analysis is a z-score, which is a measure of the difference between the observed and the expected mean (or median) expression values for a gene set. The P value related to the z-score was corrected for multiple testing using Benjamini-Hochberg false discovery rate (FDR) method. A module is “positively enriched” in a sample if it has a positive z-score with a corrected P-value < 0.05 and is “negatively enriched” if the z-score is negative with a corrected P-value < 0.05[11, 13, 17]. Besides the enrichment condition for individual samples, we also used the enrichment values for pathway clustering and principle component analysis as described [14, 17]. The results were visualized as heat maps in Gitools, which is useful for identification and interpretation of the enrichment patterns among the samples.

The KEGG pathway modules were downloaded at http://www.genome.jp/kegg/pathway.html. We investigated a total of 294 signaling pathways in the KEGG databases. For each pathway, we identified all the related genes. By mapping the gene names in the gene sets identified using KEGG pathways and the gene names in the TCGA dataset and Rembrandt dataset, we extracted the gene expression profiles for each of the 294 pathways from the 529 tumor samples in training set and the 228 tumor samples in validation set.


Conclusions

The resolution limit of modularization algorithms is a major impediment for the search of computational algorithms that are capable of detecting biologically relevant modules in molecular networks. Our method showed better accuracy in modularization and demonstrated its ability to find smaller modules on synthetic LFR networks mimicking molecular networks and real protein-protein interaction networks. The topological quality and functional significance of the modules realized after applying our method were greatly improved over the existing algorithms. The refinement algorithm developed here is a simple and incremental approach that can extend to other quality-maximizing module detection algorithms to improve the effects of the resolution limit. One could further investigate the convergence properties of our algorithm, the application in overlapping clusters and the effect of the quality loss threshold.


Methods

Plant materials and experimental design

The low Cd-accumulative cultivar “Shennong 315” (O. s. japonica, short for S315) and high Cd-accumulative cultivar “Shendao 47” (O. s. japonica, short for S47) were used as plant materials. All the seeds were obtained from the Germplasm Resources Bank of Liaoning Province with the access number of Liaoshendao[2001]No.96 and Liaoshendao[2010]No.235 for S315 and S47, respectively. The experiment was performed in an experimental greenhouse located in Northeast Agricultural University. At three true-leaf stage, rice seedlings were transplanted into greenhouse with conventional density, illumination and fertilization strategy. A total of 60 rice seedlings (including 30 seedlings of S315 and S47 each) were used as plant materials. Each rice variety (30 seedlings) was randomly divided into two pools (15 plants for each), one of which was filled with Cd 2+ -free muddy water (control group, marked as C) and the other one was treated with CdCl2·2.5H2O (10 mg/Kg) until maturity (Cd treatment group, marked as T). In total, four groups were designed, including C-S315, T-S315, C-S47, and T-S47. The samples of the first node (unelongated nodes, marked as A, Fig. 1), panicle node (marked as B, Fig. 1), and grains were collected at grain-filling stage for Cd content determination with five biological repetitions (three technical repetitions for each). All the stem nodes samples (the first and panicle nodes) were collected for transcriptome analysis and marked as C-S315-A, T-S315-A, C-S315-B, T-S315-B, C-S47-A, T-S47-A, C-S47-B, and T-S47-B, respectively, and three biological replicates were set for each group (each biological replicate contained three individuals). All fresh samples were stored at −80 °C until assayed.

Determination of total Cd concentrations

To determine the Cd concentration in node A, node B, and rice grains, an atomic absorption spectrophotometer (AAS) was used according to the instructions. Briefly, fresh tissues were shredded, dried and powdered. 100 mg of powder was treated with 1 mL HNO3 and was diluted in 20 mL ultrapure water. Standard Cd solution (CdCl2) was used as quality control samples.

Total RNA extraction and mRNA libraries construction

The total RNA was extracted from stem nodes tissues using an RNAprep pure Plant Kit (Tiangen, China). The RNA quality was evaluated using gel electrophoresis and Nanodrop (Thermo, USA). Equal RNA samples from three individuals in each group were pooled to one composite sample (as a biological repetition), and 3 composite samples were prepared in each group (n = 24 samples) accordingly. All the RNA samples were reversely transcribed to cDNA samples using a QuantScript RT Kit (Tiangen, China). The sequence libraries were then constructed using mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, China) according to the manufacturer’s instruction. Library quality was evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Finally, an Illumina HiSeq X sequencing platform (a pair-end 2×150 bp mode) was used to obtain sequencing data.

MRNA sequence data processing

The quality of raw sequencing data (.fastq format) was controlled using the FastQC (version 0.11.5, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low quality reads and adaptor reads were removed from raw data and the clean data were assembled and compared to the reference genome of rice (IRGSP-1.0.28, http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/) using hisat2 (http://ccb.jhu.edu/software/hisat2). The value of FPKM (expected number of Fragments Per kb per Millions reads) of reads was calculated using Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/cufflinks/). Principal component analysis (PCA) and Pearson’s correlation analysis were performed based on the FPKM. The differentially expressed genes (DEGs) were identified using DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html) 49 , with the criteria of p < 0.05 and |log2(Fold Change, FC) | ≥ 2. Genes with log2FC > 2 and log2FC < −2 were identified as up- and down-regulated DEGs, respectively. Hierarchical clustering based on the expression profiles of DEGs was presented by pheatmap (version 1.0.10 https://cran.r-project.org/web/packages/pheatmap/index.html).

WGCNA analyses for DEGs

The R package WGCNA (v1.61 https://cran.r-project.org/web/packages/WGCNA/index.html) was employed for the analysis of DEGs’ co-expression module 50 . The WGCNA parameters of soft threshold power of the adjacency matrix and the criteria of correlation coefficient square of eigengenes were defined according to the approximate scale-free topology preconditions and the criteria of cut-off of ≥30 genes and cut height = 0.15. The adjacency matrix dissimilarity was 0.2. Then, the WGCNA modules (co-expression network) of eigengenes were identified and the networks correlated with agronomic traits were identified with the criterion of stability correlation p ≤ 0.05. The modules with gene significance (Pearson’s correlation coefficient) ≥0.6 for agronomic traits (Cd treatment, Cd accumulation and different tissue nodes) were retained for further analyses.

GO and KEGG enrichment analysis

The DEGs in modules correlated with the agronomic traits were separately subjected to the enrichment analysis for Gene Ontoloy (GO http://www.Geneontology.org/) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways 51 . Significant GO biological processes (BP) and KEGG pathways were identified with the criterion of p < 0.05.

QRT-PCR gene expression analysis

qRT-PCR analysis was performed to verify the expression of candidate DEGs. Primers of the candidate DEGs were designed using Primer Premier 5.0 (http://www.PremierBiosoft.com). The 20 μL reaction volume contained 2 μL of diluted cDNA, 0.5 μL of forward and reverse primers (10 μM), 10 μL of 2×POWRUP SYBR MASTER MIX (Thermo, USA) and 7 μL of dd H2O. The PCR amplification were performed on an Eppendorf Mastercycler pro PCR System (Eppendorf, Germany) with 95 °C for 5 min, followed by 40 cycles of 95 °C for 15 s, 58 °C for 30 s, then followed by 72 °C for 5 min. The relative quantification was calculated by 2 −ΔΔCT method. Three independent biological replicates were designed here.

Statistical analysis

Statistical analysis was performed using GraphPad Prism 6 (https://www.graphpad.com/support/prism-6-updates/). All experimental data were expressed as mean ± standard deviation (SD), and differences between groups or treatments were analyzed using the unpaired t-test. Differences across tissues were analyzed using one-way ANOVA test. P < 0.05 was set as significant threshold for statistical differences.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


Abstract

Biological soil crusts (biocrusts) are widely distributed in arid and semi-arid environments worldwide. The microbiome metabolic pathways of biocrusts contribute to important biogeochemical processes that improve the physicochemical properties of the surface soil. However, the differences in microbial processes among different types of biocrusts have been poorly studied by metagenomic analyses. In this study, we compared two types of biocrusts (bacterial-dominated biocrusts and moss-dominated biocrusts) using shotgun metagenomic sequencing. Our results showed that Actinobacteria was the most abundant phylum in the microbiomes of bacterial and moss biocrusts, even though the two biocrusts differed in the composition of the following other abundant phyla Proteobacteria, Acidobacteria, Cyanobacteria, Planctomycetes and Bacteroidetes. The profile of the C- and N- related metabolic pathways of the metagenome differed between the bacterial and moss biocrusts. The results showed that the genes encoding carbon monoxide dehydrogenase were more abundant than the gene encoding the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) involved in the Calvin cycle, which is actually the main metabolic pathway for carbon fixation in both biocrusts. Low diversity in N2 fixation pathways appears to be a distinguishing feature of biocrust microbiomes, while nitrogen reduction dominated the metabolic networks of the two biocrusts. The microbiome of bacterial biocrusts rich in assimilatory nitrate reduction genes, while the microbiome of moss biocrusts was rich in dissimilatory nitrate reduction genes. Amongst the (bio-)chemical parameters it is total organic carbon(TOC) that differentiates between the bacterial and moss biocrusts. Our study suggests that the biocrust types have significant effects on the TOC content and taxonomic, gene and metabolic diversity.


Modules in BMSc

The Bachelor of Medical Sciences (BMSc) Program is the combination of all the modules that lead to graduation with BMSc degrees. Admission to the BMSc Program occurs in Year 3 and only students admitted to Year 3 BMSc can pursue modules that lead to graduation with BMSc degrees.

Which Modules lead to BMSc degrees?

Honours Specialization modules in BMSc

There are 21 Honours Specialization modules which lead to graduation with BMSc (Honours) degrees and only students in Years 3 and 4 BMSc can register in these modules.

Enrollment in Year 3 and 4 of each Honours Specialization module is limited due to the capstone course required in Year 4:

  • 20 Honours Specialization modules contain a 4000-level Research Project as the capstone course
  • The Honours Specialization in IMS requires a 4000-level advanced lab half course and a selected topics half course as the capstone courses (see Medical Sciences 4900F/G and 4930F/G)

If more students apply for admission to a particular Honours Specialization module than there are spaces available, then admission to the Honours Specialization becomes competitive:

  • see Admission to Year 3 BMSc for information about admission to Honours Specialization modules in Year 3 (e.g. maximum capacity and competitive averages for admission to each module, etc.)
  • see Admission to Year 4 BMSc for information about admission to Year 4 of the Honours Specialization modules (e.g. maximum capacity and competitive Weighted Averages for admission to each module, etc.)

See the Academic Calendar for the complete listing of modules offered by the basic medical science departments.

Double Majors in BMSc

Double Majors can be completed in both BMSc (Honours) and BMSc (non-honours) degrees, provided both Major modules are selected from the 9 Major modules offered by the basic medical science departments. The only difference between Double Majors in a BMSc (Honours) degree and Double Majors in a BMSc (non-honours) degree is the level of marks achieved in the modular courses. See the Graduation Requirements for Honours Bachelor Degrees and the Graduation Requirements for Bachelor Degrees (Four-Year).

Only students in Year 3 and 4 BMSc can register in Double Majors that lead to graduation with BMSc (Honours) and BMSc (non-honours) degrees:

  • a BMSc (non-honours) degree is granted if the average on the 6.0 courses required for one or both Majors is less than 70% and/or a mark less than 60% is achieved in a modular course in one or both of the Major modules and/or or if a failing grade is achieved in any course

Enrollment in Double Majors is not limited as none of the Majors contain a capstone course in Year 4:

  • the 4000-level capstone courses (Research Projects and Medical Sciences 4900F/G + 4930F/G) can only be taken by students in the Honours Specialization modules

Most BMSc students completing Double Majors will find that the same courses appear in both Major modules (e.g. Biochemistry 2280A shows up in both Majors):

  • a maximum of 1.0 "common course" can be counted toward both modules -- see the Common Course Policy
  • see Admission to Year 3 BMSc and Admission to Year 4 BMSc for information about admission to the Double Majors in Years 3 and 4

See the Academic Calendar for the complete listing of modules offered by the basic medical science departments.

Specialization in Interdisciplinary Medical Sciences (IMS)

There is only 1 Specialization module available in the BMSc Program - Specialization in IMS - and only students registered in Years 3 and 4 BMSc may register in this module.

Very few students pursue a Specialization in IMS since this module leads to graduation with a non-honours BMSc degree. Since most students in the BMSc Program meet and/or exceed the marks/averages required to register in Honours degrees, students are strongly encouraged to pursue either Honours Specialization modules or Double Majors.

Enrollment in the Specialization in IMS is not limited as this module does not contain a capstone course in Year 4

  • the 4000-level capstone courses Medical Sciences 4900F/G + 4930F/G) cannot be taken by students in the Specialization in IMS.
  • see Admission to Year 3 BMSc and Admission to Year 4 BMSc for information about admission to the Specialization in IMS in Years 3 and 4

See the Academic Calendar for the complete listing of modules offered by the basic medical science departments

Discipline-specific or interdisciplinary modules?

The decision to pursue a discipline-specific module or an IMS module is a personal decision for each student. Students seeking admission to graduate and/or professional programs after their BMSc degrees are encouraged to investigate whether their choice of discipline-specific or interdisciplinary modules will influence their eligibility.

Discipline-specific modules

Modules that focus on one or two specific basic medical science disciplines in Years 3 and 4 are referred to as "discipline-specific" modules. Examples of how the discipline-specific modules differ from the IMS modules are as follows:

  • discipline-specific modules are more structured than IMS modules
  • a Research Project is undertaken in Year 4 by students in discipline-specific Honors Specialization modules

Interdisciplinary modules in BMSc

In Years 3 and 4 of the Interdisciplinary Medical Sciences (IMS) modules, at least two basic medical science disciplines must be studied and each student chooses the disciplines to be studied.

  • rather than a Research Project in Year 4, students in the Honours Specialization in IMS take Medical Sciences 4900F/G (lab course) and 4930F/G (lecture course)in which a clinical condition/disease is considered from an interdisciplinary perspective
  • students in the Major in IMSare required to take Medical Sciences 4931F/G to gain insight into the study of a clinical condition from the lens of the various disciplines.

Which to pursue: Honours Specialization or Double Majors? or Specialization?

Students are encouraged to pursue either an Honours Specialization module or Double Majors within the BMSc Program since these lead to graduation with a BMSc Honours degree. Students completing a Specialization module will complete a BMSc degree (non-honours). W

Students often ask if an Honours Specialization module will benefit them more than Double Majors upon graduation with a BMSc degree. An Honours Specialization module will benefit you if the program/career to which you wish to apply after graduation either prefers or requires an Honours Specialization module.

Why consider an Honours Specialization module?

You might wish to consider an Honours Specialization module if:

  • you want to graduate with an Honours degree (might be required or preferred for your career path)
  • you would like to take a capstone course in Year 4: either (i) a Research Project in discipline-specific Honours Specialization modules, or (ii) Medical Sciences 4900F/G and 4930F/G for the Honours Specialization in IMS

Some graduate programs (Masters, PhD) at various universities may prefer students who have completed a research project in their undergraduate degree, while other graduate programs may simply want students to possess an Honours degree.

You'll need to contact the specific programs to which you wish to apply for answers to questions like:

  • is an honours degree required (or preferred) for admission?
  • am I at an advantage for admission if I complete an Honours Specialization module vs. Double Majors?
  • am I a more competitive candidate if I complete a Research Project (only available in discipline-specific Honours Specialization modules)

Why consider Double Majors?

Double Majors lead to graduation with either a BMSc Honours degree or a BMSc degree (non-honours). The Majors are the same in the two degree types (i.e. the required courses are exactly the same) but students need higher marks to graduate with the Honours degree (e.g. at least 60% in each modular course and an average of 70% on all courses in each Major - see details here).

You might wish to consider Double Majors if:

  • you want to study two disciplines within the basic medical sciences but there is not an Honours Specialization module that contains courses from the two disciplines
    • examples of modules that contain more than one discipline include Honours Specialization in IMS and Honours Specialization in Biochemistry and Cancer Biology

    Registration in Double Majors in Year 4 is not limited to a particular number of students in Year 4 and you will be admitted to Year 4 Double Majors from Year 3 BMSc as long as you have the prerequisites to take the required 4000-level courses.

    Keep in mind that Double Majors in the BMSc Program almost always have "common courses" - modular courses that show up in both modules - and that there is a policy that specifies that a maximum of 1.0 common course can be used toward both modules (see details of the Common Course Policy).

    Why (or why not) consider a Specialization in IMS?

    A Specialization in IMS leads only to a non-honours BMSc degree and you need to determine if any program/career in which you might be interested after your degree either requires or prefers an Honours degree.

    You might wish to consider a Specialization in IMS if:

      your career path does not require or prefer an Honours degree

    We do not encourage you to complete the Specialization in IMS since you cannot graduate with an Honours degree. Very few BMSc students graduate with the Specialization in IMS for this reason.


    Adding Items to a Learning Module

    Now that you have created a Learning Module, it is time to add an item to it. An item can be any of the following:

    • Text you enter
    • An attached file in a variety of formats, including HTML, .jpg, or .gif
    • A series of files that are linked together such as a web site
    • An embedded file such as a Flash animation or YouTube video
    • A combination of options listed above

    An item can be any type of formatted text, such as reference materials, directions, a reading list, or lecture notes. Images, external links, tables, bulleted lists, and file attachments can also be added.

    QUICK STEPS: adding items to a Learning Module

    1. In Edit Mode, on the Course Menu, click the Content Area containing the Learning Module.
    2. On the Content Area page, click the Learning Module’s title.
    3. On the Learning Module’s Action Bar, point to Build Content and click Item.
    4. On the Create Item page, enter a Name. The Name will appear in the Table of Contents in the Learning Module.
    5. Enter text in the Text box. Use formatting options to select font face, size, alignment and color. Use the Text Editor to insert images, embed multimedia files and spell check.
    6. Add an attached file by clicking Browse My Computer, or Browse Course Files.
    7. Select the Options for availability, tracking, and date and time restrictions.
    8. Click Submit.

    You can enter a name for a file attachment, rather than use the file name. If you do not enter a name, the file name will be used.


    Watch the video: What is the difference between modules and submodules? (January 2022).